EcoliWiki - User contributions [en]

PMID:12081949

2008-02-06T15:08:27Z

172.16.48.28: New PMID: Page!

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 '''Corre, J and Louarn, JM''' (2002) Evidence from terminal recombination gradients that FtsK uses replichore polarity to control chromosome terminus positioning at division in Escherichia coli.''J. Bacteriol.'' '''184''':3801-7

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|{{TableHeadingColor}} |'''Abstract''' || Chromosome dimers in Escherichia coli are resolved at the dif locus by two recombinases, XerC and XerD, and the septum-anchored FtsK protein. Chromosome dimer resolution (CDR) is subject to strong spatiotemporal control: it takes place at the time of cell division, and it requires the dif resolution site to be located at the junction between the two polarized chromosome arms or replichores. Failure of CDR results in trapping of DNA by the septum and RecABCD recombination (terminal recombination). We had proposed that dif sites of a dimer are first moved to the septum by mechanisms based on local polarity and that normally CDR then occurs as the septum closes. To determine whether FtsK plays a role in the mobilization process, as well as in the recombination reaction, we characterized terminal recombination in an ftsK mutant. The frequency of recombination at various points in the terminus region of the chromosome was measured and compared with the recombination frequency on a xerC mutant chromosome with respect to intensity, the region affected, and response to polarity distortion. The use of a prophage excision assay, which allows variation of the site of recombination and interference with local polarity, allowed us to find that cooperating FtsK-dependent and -independent processes localize dif at the septum and that DNA mobilization by FtsK is oriented by the polarity probably due to skewed sequence motifs of the mobilized material.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12081949 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:12107130

2008-02-06T15:08:21Z

172.16.48.28: New PMID: Page!

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 '''Kim, AD, Baker, AS, Dunaway-Mariano, D, Metcalf, WW, Wanner, BL and Martin, BM''' (2002) The 2-aminoethylphosphonate-specific transaminase of the 2-aminoethylphosphonate degradation pathway.''J. Bacteriol.'' '''184''':4134-40

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|{{TableHeadingColor}} |'''Abstract''' || The 2-aminoethylphosphonate transaminase (AEPT; the phnW gene product) of the Salmonella enterica serovar Typhimurium 2-aminoethylphosphonate (AEP) degradation pathway catalyzes the reversible reaction of AEP and pyruvate to form phosphonoacetaldehyde (P-Ald) and L-alanine (L-Ala). Here, we describe the purification and characterization of recombinant AEPT. pH rate profiles (log V(m) and log V(m)/K(m) versus pH) revealed a pH optimum of 8.5. At pH 8.5, K(eq) is equal to 0.5 and the k(cat) values of the forward and reverse reactions are 7 and 9 s(-1), respectively. The K(m) for AEP is 1.11 +/- 0.03 mM; for pyruvate it is 0.15 +/- 0.02 mM, for P-Ald it is 0.09 +/- 0.01 mM, and for L-Ala it is 1.4 +/- 0.03 mM. Substrate specificity tests revealed a high degree of discrimination, indicating a singular physiological role for the transaminase in AEP degradation. The 40-kDa subunit of the homodimeric enzyme is homologous to other members of the pyridoxalphosphate-dependent amino acid transaminase superfamily. Catalytic residues conserved within well-characterized members are also conserved within the seven known AEPT sequences. Site-directed mutagenesis demonstrated the importance of three selected residues (Asp168, Lys194, and Arg340) in AEPT catalysis.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12107130 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:12079335

2008-02-06T15:08:16Z

172.16.48.28: New PMID: Page!

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 '''Delagoutte, E, Fuchs, RP and Bertrand-Burggraf, E''' (2002) The isomerization of the UvrB-DNA preincision complex couples the UvrB and UvrC activities.''J. Mol. Biol.'' '''320''':73-84

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|{{TableHeadingColor}} |'''Abstract''' || In Escherichia coli nucleotide excision repair, the UvrB-DNA preincision complex plays a key role, linking adduct recognition to incision. We previously showed that the efficiency of the incision is inversely related to the stability of the preincision complex. We postulated that an isomerization reaction converts [UvrB-DNA], stable but incompetent for incision, into the [UvrB-DNA]' complex, unstable and competent for incision. Here, we identify two parameters, negative supercoiling and presence of a nick at the fifth phosphodiester bond 3' to the lesion, that accelerate the isomerization leading to an increasing incision efficiency. We also show that the [UvrB-DNA] complex is more resistant to a salt concentration increase than the [UvrB-DNA]' complex. Finally, we report that the [UvrB-DNA]' is recognized by UvrC. These data suggest that the isomerization reaction leads to an exposure of single-stranded DNA around the lesion. This newly exposed single-stranded DNA serves as a binding site and substrate for the UvrC endonuclease. We propose that the isomerization reaction is responsible for coupling UvrB and UvrC activities and that this reaction corresponds to the binding of ATP.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12079335 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:12065427

2008-02-06T15:08:11Z

172.16.48.28: New PMID: Page!

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 '''Davey, MJ, Fang, L, McInerney, P, Georgescu, RE and O'Donnell, M''' (2002) The DnaC helicase loader is a dual ATP/ADP switch protein.''EMBO J.'' '''21''':3148-59

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|{{TableHeadingColor}} |'''Abstract''' || Helicases are transferred to replication origins by helicase loading factors. The Escherichia coli DnaC and eukaryotic Cdc6/18 helicase loaders contain ATP sites and are both members of the AAA+ family. One might expect that ATP is required for helicase loading; however, this study on DnaC illustrates that ATP is not actually needed for DnaC to load helicase onto single-strand DNA (ssDNA). In fact, it seems to be a paradox that after transfer of helicase to DNA, DnaC-ATP inhibits helicase action. In addition, ATP is required for DnaC function at an early step in oriC replication in which ATP stimulates ssDNA binding by DnaC, leading to expansion of the ssDNA bubble at the origin. Two cofactors, ssDNA and DnaB, trigger hydrolysis of ATP, converting DnaC to the ADP form that no longer inhibits DnaB. These observations have led to the idea that DnaC is a 'dual' switch protein, where both the ATP and the ADP forms are sequentially required for replication. This dual switching process may underlie the sensitivity of DnaB to even small fluctuations in DnaC levels.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12065427 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:12093725

2008-02-06T15:08:06Z

172.16.48.28: New PMID: Page!

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 '''Cruz-Ramos, H, Crack, J, Wu, G, Hughes, MN, Scott, C, Thomson, AJ, Green, J and Poole, RK''' (2002) NO sensing by FNR: regulation of the Escherichia coli NO-detoxifying flavohaemoglobin, Hmp.''EMBO J.'' '''21''':3235-44

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|{{TableHeadingColor}} |'''Abstract''' || Nitric oxide (NO) is a signalling and defence molecule of major importance in biology. The flavohaemoglobin Hmp of Escherichia coli is involved in protective responses to NO. Because hmp gene transcription is repressed by the O(2)-responsive regulator FNR, we investigated whether FNR also senses NO. The [4Fe-4S](2+) cluster of FNR is oxygen labile and controls protein dimerization and site-specific DNA binding. NO reacts anaerobically with the Fe-S cluster of purified FNR, generating spectral changes consistent with formation of a dinitrosyl-iron-cysteine complex. NO-inactivated FNR can be reconstituted, suggesting physiological relevance. FNR binds at an FNR box within the hmp promoter (P(hmp)). FNR samples inactivated by either O(2) or NO bind specifically to P(hmp), but with lower affinity. Dose-dependent up-regulation of P(hmp) in vivo by NO concentrations of pathophysiological relevance is abolished by fnr mutation, and NO also modulates expression from model FNR-regulated promoters. Thus, FNR can respond to not only O(2), but also NO, with major implications for global gene regulation in bacteria. We propose an NO-mediated mechanism of hmp regulation by which E.coli responds to NO challenge.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12093725 PubMed]
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{|class = 'sortable' {{Prettytable}} id='228452'
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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PMID:12135348

2008-02-06T15:08:00Z

172.16.48.28: New PMID: Page!

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 '''Gabelli, SB, Bianchet, MA, Ohnishi, Y, Ichikawa, Y, Bessman, MJ and Amzel, LM''' (2002) Mechanism of the Escherichia coli ADP-ribose pyrophosphatase, a Nudix hydrolase.''Biochemistry'' '''41''':9279-85

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|{{TableHeadingColor}} |'''Abstract''' || Escherichia coli ADP-ribose (ADPR) pyrophosphatase (ADPRase), a Nudix enzyme, catalyzes the Mg(2+)-dependent hydrolysis of ADP-ribose to AMP and ribose 5-phosphate. ADPR hydrolysis experiments conducted in the presence of H(2)(18)O and analyzed by electrospray mass spectrometry showed that the ADPRase-catalyzed reaction takes place through nucleophilic attack at the adenosyl phosphate. The structure of ADPRase in complex with Mg(2+) and a nonhydrolyzable ADPR analogue, alpha,beta-methylene ADP-ribose, reveals an active site water molecule poised for nucleophilic attack on the adenosyl phosphate. This water molecule is activated by two magnesium ions, and its oxygen contacts the target phosphorus (P-O distance of 3.0 A) and forms an angle of 177 degrees with the scissile bond, suggesting an associative mechanism. A third Mg(2+) ion bridges the two phosphates and could stabilize the negative charge of the leaving group, ribose 5-phosphate. The structure of the ternary complex also shows that loop L9 moves fully 10 A from its position in the free enzyme, forming a tighter turn and bringing Glu 162 to its catalytic position. These observations indicate that as part of the catalytic mechanism, the ADPRase cycles between an open (free enzyme) and a closed (substrate-metal complex) conformation. This cycling may be important in preventing nonspecific hydrolysis of other nucleotides.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12135348 PubMed]
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{|class = 'sortable' {{Prettytable}} id='228451'
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.W47a9cd4fd9727&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
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PMID:11972788

2008-02-06T15:07:55Z

172.16.48.28: New PMID: Page!

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 '''Correnti, J, Munster, V, Chan, T and Woude, M''' (2002) Dam-dependent phase variation of Ag43 in Escherichia coli is altered in a seqA mutant.''Mol. Microbiol.'' '''44''':521-32

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|{{TableHeadingColor}} |'''Abstract''' || In Escherichia coli, phase variation of the outer membrane protein Ag43 encoded by the agn43 gene is mediated by DNA methylation and the global regulator OxyR. Transcription of agn43 occurs (ON phase) when three Dam target sequences in the agn43 regulatory region are methylated, which prevents the repressor OxyR from binding. Conversely, transcription is repressed (OFF) when these Dam target sequences are unmethylated and OxyR binds. A change in expression phase requires a concomitant change in the DNA methylation state of these Dam target sequences. To gain insight into the process of inheritance of the expression phase and the DNA methylation state, protein-DNA interactions at agn43 were examined. Binding of OxyR at agn43 was sufficient to protect the three GATC sequences contained within its binding site from Dam-dependent methylation in vitro, suggesting that no other factors are required to maintain the unmethylated state and OFF phase. To maintain the methylated state of the ON phase, however, Dam must access the hemimethylated agn43 region after DNA replication, and OxyR binding must not occur. OxyR bound hemimethylated agn43 DNA, but the affinity was severalfold lower than for unmethylated DNA. This presumably contributes to the maintenance of the methylated state but, at the same time, may allow for infrequent OxyR binding and a switch to the OFF phase. Hemimethylated agn43 DNA was also a binding substrate for the sequestration protein SeqA. Thus, SeqA, OxyR and Dam may compete for the same hemimethylated agn43 DNA that is formed after DNA replication in an ON phase cell. In isolates with a mutant seqA allele, agn43 phase variation rates were altered and resulted in a bias to the OFF phase. In part, this can be attributed to the observed decrease in the level of DNA methylation in the seqA mutant.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11972788 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:12100995

2008-02-06T15:07:49Z

172.16.48.28: New PMID: Page!

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 '''Engel, CK, Chen, L and Privé, GG''' (2002) Stability of the lactose permease in detergent solutions.''Biochim. Biophys. Acta'' '''1564''':47-56

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|{{TableHeadingColor}} |'''Abstract''' || Protein stability, as measured by irreversible protein aggregation, is one of the central difficulties in the handling of detergent-solubilized membrane proteins. We present a quantitative analysis of the stability of the Escherichia coli lactose (lac) permease and a series of lac permease fusion proteins containing an insertion of cytochrome(b562), T4 lysozyme or beta-lactamase in the central hydrophilic loop of the permease. The stability of the proteins was evaluated under a variety of storage conditions by both a qualitative SDS-PAGE assay and by a quantitative hplc assay. Long-chain maltoside detergents were more effective at maintaining purified protein in solution than detergents with smaller head groups and/or shorter alkyl tails. A full factorial experiment established that the proteins were insensitive to sodium chloride concentrations, but greatly stabilized by glycerol, low temperature and the combination of glycerol and low temperature. The accurate quantitation of the protein by absorbance spectroscopy required exclusion of all contact with clarified polypropylene or polyvinyl chloride (PVC) materials. Although some of the fusion proteins were more prone to aggregation than the wild-type permease, the stability of a fusion protein containing a cytochrome(b562) insertion was indistinguishable from that of native lac permease.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12100995 PubMed]
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{|class = 'sortable' {{Prettytable}} id='228449'
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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PMID:14499611

2008-02-06T15:07:44Z

172.16.48.28: New PMID: Page!

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 '''Zhang, RG, Andersson, CE, Skarina, T, Evdokimova, E, Edwards, AM, Joachimiak, A, Savchenko, A and Mowbray, SL''' (2003) The 2.2 A resolution structure of RpiB/AlsB from Escherichia coli illustrates a new approach to the ribose-5-phosphate isomerase reaction.''J. Mol. Biol.'' '''332''':1083-94

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|{{TableHeadingColor}} |'''Abstract''' || Ribose-5-phosphate isomerases (EC 5.3.1.6) interconvert ribose 5-phosphate and ribulose 5-phosphate. This reaction permits the synthesis of ribose from other sugars, as well as the recycling of sugars from nucleotide breakdown. Two unrelated types of enzyme can catalyze the reaction. The most common, RpiA, is present in almost all organisms (including Escherichia coli), and is highly conserved. The second type, RpiB, is present in some bacterial and eukaryotic species and is well conserved. In E.coli, RpiB is sometimes referred to as AlsB, because it can take part in the metabolism of the rare sugar, allose, as well as the much more common ribose sugars. We report here the structure of RpiB/AlsB from E.coli, solved by multi-wavelength anomalous diffraction (MAD) phasing, and refined to 2.2A resolution. RpiB is the first structure to be solved from pfam02502 (the RpiB/LacAB family). It exhibits a Rossmann-type alphabetaalpha-sandwich fold that is common to many nucleotide-binding proteins, as well as other proteins with different functions. This structure is quite distinct from that of the previously solved RpiA; although both are, to some extent, based on the Rossmann fold, their tertiary and quaternary structures are very different. The four molecules in the RpiB asymmetric unit represent a dimer of dimers. Active-site residues were identified at the interface between the subunits, such that each active site has contributions from both subunits. Kinetic studies indicate that RpiB is nearly as efficient as RpiA, despite its completely different catalytic machinery. The sequence and structural results further suggest that the two homologous components of LacAB (galactose-6-phosphate isomerase) will compose a bi-functional enzyme; the second activity is unknown.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14499611 PubMed]
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{|class = 'sortable' {{Prettytable}} id='228448'
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.W47a9cd3f6b970&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
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PMID:14597655

2008-02-06T15:07:38Z

172.16.48.28: New PMID: Page!

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 '''Gutiérrez-Ríos, RM, Rosenblueth, DA, Loza, JA, Huerta, AM, Glasner, JD, Blattner, FR and Collado-Vides, J''' (2003) Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles.''Genome Res.'' '''13''':2435-43

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|{{TableHeadingColor}} |'''Abstract''' || The transcriptional network of Escherichia coli may well be the most complete experimentally characterized network of a single cell. A rule-based approach was built to assess the degree of consistency between whole-genome microarray experiments in different experimental conditions and the accumulated knowledge in the literature compiled in RegulonDB, a data base of transcriptional regulation and operon organization in E. coli. We observed a high and statistical significant level of consistency, ranging from 70%-87%. When effector metabolites of regulatory proteins are not considered in the prediction of the active or inactive state of the regulators, consistency falls by up to 40%. Similarly, consistency decreases when rules for multiple regulatory interactions are altered or when "on" and "off" entries were assigned randomly. We modified the initial state of regulators and evaluated the propagation of errors in the network that do not correlate linearly with the connectivity of regulators. We interpret this deviation mainly as a result of the existence of redundant regulatory interactions. Consistency evaluation opens a new space of dialogue between theory and experiment, as the consequences of different assumptions can be evaluated and compared.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14597655 PubMed]
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{|class = 'sortable' {{Prettytable}} id='228447'
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.G47a9cd3a1194e&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
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PMID:14523019

2008-02-06T15:07:33Z

172.16.48.28: New PMID: Page!

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 '''Georlette, D, Blaise, V, Dohmen, C, Bouillenne, F, Damien, B, Depiereux, E, Gerday, C, Uversky, VN and Feller, G''' (2003) Cofactor binding modulates the conformational stabilities and unfolding patterns of NAD(+)-dependent DNA ligases from Escherichia coli and Thermus scotoductus.''J. Biol. Chem.'' '''278''':49945-53

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || DNA ligases are important enzymes required for cellular processes such as DNA replication, recombination, and repair. NAD(+)-dependent DNA ligases are essentially restricted to eubacteria, thus constituting an attractive target in the development of novel antibiotics. Although such a project might involve the systematic testing of a vast number of chemical compounds, it can essentially gain from the preliminary deciphering of the conformational stability and structural perturbations associated with the formation of the catalytically active adenylated enzyme. We have, therefore, investigated the adenylation-induced conformational changes in the mesophilic Escherichia coli and thermophilic Thermus scotoductus NAD(+)-DNA ligases, and the resistance of these enzymes to thermal and chemical (guanidine hydrochloride) denaturation. Our results clearly demonstrate that anchoring of the cofactor induces a conformational rearrangement within the active site of both mesophilic and thermophilic enzymes accompanied by their partial compaction. Furthermore, the adenylation of enzymes increases their resistance to thermal and chemical denaturation, establishing a thermodynamic link between cofactor binding and conformational stability enhancement. Finally, guanidine hydrochloride-induced unfolding of NAD(+)-dependent DNA ligases is shown to be a complex process that involves accumulation of at least two equilibrium intermediates, the molten globule and its precursor.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14523019 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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<protect>

{|class = 'sortable' {{Prettytable}} id='228446'
|- {{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.A47a9cd34a433d&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12713816

2008-02-06T15:07:27Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Garibyan, L, Huang, T, Kim, M, Wolff, E, Nguyen, A, Nguyen, T, Diep, A, Hu, K, Iverson, A, Yang, H and Miller, JH''' (2003) Use of the rpoB gene to determine the specificity of base substitution mutations on the Escherichia coli chromosome.''DNA Repair (Amst.)'' '''2''':593-608

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || Mutations in the rpoB gene of Escherichia coli result in resistance to the antibiotic rifampicin (Rif(r)) by altering the beta subunit of RNA polymerase. Previous studies have identified 39 single base substitutions in the rpoB gene that lead to Rif(r) at 37 degrees C and an additional two mutations that result in temperature sensitive cells. We have extended this work and identified an additional 30 single base substitutions that result in the Rif(r) phenotype. With these mutations the rpoB/Rif(r) system now allows the monitoring of 69 base substitutions at 37 degrees at 37 sites (base pairs) distributed among 24 coding positions. Each of the six possible base substitutions is represented by 8-17 mutations. More than 90% of the mutations are within a small enough region of the rpoB gene to allow PCR amplification with a single pair of oligonucleotide primers, followed by sequencing with a single primer, leading to rapid analysis of numerous mutations. The remaining mutations can be monitored using an additional primer pair. To calibrate this system we sequenced over 500 mutations in rpoB occurring spontaneously or generated by different mutagens and mutators with known specificity. These results show that rpoB/Rif(r) is an accurate and easy to employ detection system, and offers the advantage of allowing analysis of mutations occurring on the chromosome rather than on an extrachromosomal element. The mutS, mutT, mutY, M mutators, as well as the mutagenic agents ethyl methanesulfonate (EMS), ultraviolet (UV) irradiation, 2-aminopurine (2AP), 5-azacytidine (5AZ), and cisplatin (CPT) gave results predicted by their characterized specificities. The number of different sequence contexts is sufficient to reveal significant hotspots among the spontaneous mutS, 2-aminopurine, ultraviolet light, 5-azacytidine, and cisplatin mutational spectra. The cisplatin distribution is particularly striking, with 68% of the mutations resulting from an A:T-->T:A transversion at a single site. Because of the conservation of key regions of RNA polymerase among many microorganisms, using the Rif(r)/rpoB system may be a general method for studying mutational processes in microorganisms without well developed genetic systems.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12713816 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='228445'
|- {{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.Y47a9cd2ed27b7&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12626396

2008-02-06T15:07:21Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Elbein, AD, Pan, YT, Pastuszak, I and Carroll, D''' (2003) New insights on trehalose: a multifunctional molecule.''Glycobiology'' '''13''':17R-27R

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Trehalose is a nonreducing disaccharide in which the two glucose units are linked in an alpha,alpha-1,1-glycosidic linkage. This sugar is present in a wide variety of organisms, including bacteria, yeast, fungi, insects, invertebrates, and lower and higher plants, where it may serve as a source of energy and carbon. In yeast and plants, it may also serve as a signaling molecule to direct or control certain metabolic pathways or even to affect growth. In addition, it has been shown that trehalose can protect proteins and cellular membranes from inactivation or denaturation caused by a variety of stress conditions, including desiccation, dehydration, heat, cold, and oxidation. Finally, in mycobacteria and corynebacteria, trehalose is an integral component of various glycolipids that are important cell wall structures. There are now at least three different pathways described for the biosynthesis of trehalose. The best known and most widely distributed pathway involves the transfer of glucose from UDP-glucose (or GDP-glucose in some cases) to glucose 6-phosphate to form trehalose-6-phosphate and UDP. This reaction is catalyzed by the trehalose-P synthase (TPS here, or OtsA in Escherichia coli ). Organisms that use this pathway usually also have a trehalose-P phosphatase (TPP here, or OtsB in E. coli) that converts the trehalose-P to free trehalose. A second pathway that has been reported in a few unusual bacteria involves the intramolecular rearrangement of maltose (glucosyl-alpha1,4-glucopyranoside) to convert the 1,4-linkage to the 1,1-bond of trehalose. This reaction is catalyzed by the enzyme called trehalose synthase and gives rise to free trehalose as the initial product. A third pathway involves several different enzymes, the first of which rearranges the glucose at the reducing end of a glycogen chain to convert the alpha1,4-linkage to an alpha,alpha1,1-bond. A second enzyme then releases the trehalose disaccharide from the reducing end of the glycogen molecule. Finally, in mushrooms there is a trehalose phosphorylase that catalyzes the phosphorolysis of trehalose to produce glucose-1-phosphate and glucose. This reaction is reversible in vitro and could theoretically give rise to trehalose from glucose-1-P and glucose. Another important enzyme in trehalose metabolism is trehalase (T), which may be involved in energy metabolism and also have a regulatory role in controlling the levels of trehalose in cells. This enzyme may be important in lowering trehalose concentrations once the stress is alleviated. Recent studies in yeast indicate that the enzymes involved in trehalose synthesis (TPS, TPP) exist together in a complex that is highly regulated at the activity level as well as at the genetic level.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12626396 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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<protect>

{|class = 'sortable' {{Prettytable}} id='228444'
|- {{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.K47a9cd28d3624&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

PMID:12739900

2008-02-06T15:07:16Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Du, X and Wang, ED''' (2003) E292 is important for the aminoacylation activity of Escherichia coli leucyl-tRNA synthetase.''J. Protein Chem.'' '''22''':71-6

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Escherichia coli leucyl-tRNA synthetase (LeuRS) has a large connecting polypeptide (CP1) inserted into its active site. It was demonstrated that the peptide bond between E292-A293 was crucial for the aminoacylation activity of E. coli LeuRS. To investigate the effect of E292 on the function of Escherichia coli LeuRS, E292 was mutated to K, F, S, D, Q and A. These mutations at 292 did not change the specific activity of the amino acid activation reaction. Though the conformational change of these mutants was not detected in CD, their aminoacylation activities were impaired to varying extents. The mutation of E to K decreased the aminoacylation activity to the largest extent. Analysis of the Km values of these mutants for the three substrates showed that the E292 was not involved in the binding of leucine and that all mutants had stronger binding with ATP.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12739900 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228443'
|- {{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.X47a9cd23cc488&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:14597652

2008-02-06T15:07:11Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Djordjevic, M, Sengupta, AM and Shraiman, BI''' (2003) A biophysical approach to transcription factor binding site discovery.''Genome Res.'' '''13''':2381-90

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Identification of transcription factor binding sites within regulatory segments of genomic DNA is an important step toward understanding of the regulatory circuits that control expression of genes. Here, we describe a novel bioinformatics method that bases classification of potential binding sites explicitly on the estimate of sequence-specific binding energy of a given transcription factor. The method also estimates the chemical potential of the factor that defines the threshold of binding. In contrast with the widely used information-theoretic weight matrix method, the new approach correctly describes saturation in the transcription factor/DNA binding probability. This results in a significant improvement in the number of expected false positives, particularly in the ubiquitous case of low-specificity factors. In the strong binding limit, the algorithm is related to the "support vector machine" approach to pattern recognition. The new method is used to identify likely genomic binding sites for the E. coli transcription factors collected in the DPInteract database. In addition, for CRP (a global regulatory factor), the likely regulatory modality (i.e., repressor or activator) of predicted binding sites is determined.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14597652 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228442'
|- {{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.C47a9cd1e988ef&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12646383

2008-02-06T15:07:05Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Stan, G, Thirumalai, D, Lorimer, GH and Brooks, BR''' (2003) Annealing function of GroEL: structural and bioinformatic analysis.''Biophys. Chem.'' '''100''':453-67

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || The Escherichia coli chaperonin system, GroEL-GroES, facilitates folding of substrate proteins (SPs) that are otherwise destined to aggregate. The iterative annealing mechanism suggests that the allostery-driven GroEL transitions leading to changes in the microenvironment of the SP constitutes the annealing action of chaperonins. To describe the molecular basis for the changes in the nature of SP-GroEL interactions we use the crystal structures of GroEL (T state), GroEL-ATP (R state) and the GroEL-GroES-(ADP)(7) (R" state) complex to determine the residue-specific changes in the accessible surface area and the number of tertiary contacts as a result of the T-->R-->R" transitions. We find large changes in the accessible area in many residues in the apical domain, but relatively smaller changes are associated with residues in the equatorial domain. In the course of the T-->R transition the microenvironment of the SP changes which suggests that GroEL is an annealing machine even without GroES. This is reflected in the exposure of Glu386 which loses six contacts in the T-->R transition. We also evaluate the conservation of residues that participate in the various chaperonin functions. Multiple sequence alignments and chemical sequence entropy calculations reveal that, to a large extent, only the chemical identities and not the residues themselves important for the nominal functions (peptide binding, nucleotide binding, GroES and substrate protein release) are strongly conserved. Using chemical sequence entropy, which is computed by classifying aminoacids into four types (hydrophobic, polar, positively charged and negatively charged) we make several new predictions that are relevant for peptide binding and annealing function of GroEL. We identify a number of conserved peptide binding sites in the apical domain which coincide with those found in the 1.7 A crystal structure of 'mini-chaperone' complexed with the N-terminal tag. Correlated mutations in the HSP60 family, that might control allostery in GroEL, are also strongly conserved. Most importantly, we find that charged solvent-exposed residues in the T state (Lys 226, Glu 252 and Asp 253) are strongly conserved. This leads to the prediction that mutating these residues, that control the annealing function of the SP, can decrease the efficacy of the chaperonin function.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12646383 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='228441'
|- {{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.A47a9cd191446b&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

PMID:12767817

2008-02-06T15:07:00Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Dutta, A, Rao, BJ and Chary, KV''' (2003) Overexpression and purification of isotopically labeled Escherichia coli MutH for NMR studies.''Protein Expr. Purif.'' '''29''':252-8

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || MutH is one of the enzymes involved in the methyl directed -GATC-based DNA repair system. We report a significantly optimized protocol to prepare isotopically (15N and/or 13C) labeled MutH in minimal medium with high yields for NMR studies. Under the various conditions that we have standardized for the affinity purification of His(6) MutH, the yield of the purified MutH has been estimated to be 35-40 mg of protein from 1liter of M9 minimal media. The yield, thus, obtained by this method is significantly higher than those of previously reported methods. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectroscopy analysis revealed that the protein was pure and existed essentially in a monomeric form. Uniformly 15N-labeled protein, thus, produced has been characterized by recording a sensitivity enhanced 2D [15N]-[1H] HSQC spectrum. The dispersion seen in 15N-1H cross-peaks indicates the presence of a well-ordered structure for MutH and proper folding of the purified protein. The spectrum confirms further the existence of MutH as a monomer.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12767817 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='228440'
|- {{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.Z47a9cd1394f69&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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{{RefHelp}}
<references/>

PMID:12890032

2008-02-06T15:06:54Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''El-Labany, S, Sohanpal, BK, Lahooti, M, Akerman, R and Blomfield, IC''' (2003) Distant cis-active sequences and sialic acid control the expression of fimB in Escherichia coli K-12.''Mol. Microbiol.'' '''49''':1109-18

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || The phase variation of type 1 fimbriation in Escherichia coli is controlled by the inversion of a 314 bp element of DNA, determined by FimB (switching in both directions) or FimE (switching from the ON-to-OFF orientation predominantly), and influenced by auxiliary factors IHF, Lrp and H-NS. The fimB gene is separated from the divergently transcribed yjhATS operon by a large (1.4 kbp) intergenic region of unknown function. Here, we show that fimB expression is regulated by multiple cis-active sequences that lie far upstream (>600 bp) of the transcription start sites for the recombinase gene. Two regions characterized further (regions 1 and 2) show sequence identity, and each coincides with a methylation-protected Dam (5'-GATC) site. Regions 1 and 2 apparently control fimB expression by an antirepression mechanism that involves additional sequences proximal to yjhA. Region 1 encompasses a 27 bp DNA sequence conserved upstream of genes known (nanAT ) or suspected (yjhBC) to be involved in sialic acid metabolism, and we show that FimB expression and recombination are suppressed by N-acetylneuraminic acid. We propose that E. coli recognizes the amino sugars as a harbinger of potential host defence activation, and suppresses the expression of type 1 fimbriae in response.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12890032 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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

{|class = 'sortable' {{Prettytable}} id='228439'
|- {{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.C47a9cd0de19f8&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:13129913

2008-02-06T15:06:49Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Eschenburg, S, Kabsch, W, Healy, ML and Schonbrunn, E''' (2003) A new view of the mechanisms of UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) and 5-enolpyruvylshikimate-3-phosphate synthase (AroA) derived from X-ray structures of their tetrahedral reaction intermediate states.''J. Biol. Chem.'' '''278''':49215-22

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) and 5-enolpyruvylshikimate-3-phosphate synthase (AroA) constitute the small enzyme family of enolpyruvyl transferases, which catalyze the chemically unusual reaction of enolpyruvyl transfer. MurA catalyzes the first step in the biosynthesis of the bacterial cell wall; AroA is the sixth enzyme of the shikimate pathway leading to the synthesis of aromatic compounds in numerous microorganisms and plants. Because both metabolic pathways are absent from mammals but essential for the growth of microorganisms, MurA and AroA are attractive targets for the development of novel antimicrobial drugs. We have determined the x-ray structures of the D305A mutant of Enterobacter cloacae MurA and the D313A mutant of Escherichia coli AroA, both of which crystallized in the presence of their substrates. The structures depict the tetrahedral reaction intermediate states of the enzymes and prove that, without the aspartate side chain, the overall addition-elimination reaction in both enzymes is halted after the addition step. The presented structures lead to a new view of the catalytic mechanism and, moreover, provide an ideal starting point for the rational design of potent inhibitors of MurA and AroA.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=13129913 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='228438'
|- {{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.B47a9cd0885d6b&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12890014

2008-02-06T15:06:43Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Postle, K and Kadner, RJ''' (2003) Touch and go: tying TonB to transport.''Mol. Microbiol.'' '''49''':869-82

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || The TonB system of Gram-negative bacteria appears to exist for the purpose of transducing the protonmotive force energy from the cytoplasmic membrane, where it is generated, to the outer membrane, where it is needed for active transport of iron siderophores, vitamin B12 and, in pathogens, iron from host-binding proteins. In this review, we bring the reader up to date on the developments in the field since the authors each wrote reviews in this journal in 1990.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12890014 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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

{|class = 'sortable' {{Prettytable}} id='228437'
|- {{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.J47a9cd0343c26&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12831884

2008-02-06T15:06:38Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Rodnina, MV and Wintermeyer, W''' (2003) Peptide bond formation on the ribosome: structure and mechanism.''Curr. Opin. Struct. Biol.'' '''13''':334-40

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || The peptidyl transferase reaction on the ribosome is catalyzed by RNA. Pre-steady-state kinetic studies using Escherichia coli ribosomes suggest that catalysis (>10(5)-fold overall acceleration) is, to a large part, a result of substrate positioning, in agreement with crystal structures of large ribosomal subunits with bound substrate or product analogs. The rate of peptide bond formation is inhibited approximately 100-fold by protonation of a single ribosomal group with a pK(a) of 7.5, indicating general acid-base catalysis and/or a pH-dependent conformational change within the active site. According to the kinetics of mutant ribosomes, these effects may be attributed to a candidate catalytic base (A2451) suggested by the crystal structure.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12831884 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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<protect>

{|class = 'sortable' {{Prettytable}} id='228436'
|- {{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.D47a9ccfe3b5e0&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12949168

2008-02-06T15:06:32Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Stancek, M, Isaksson, LA and Rydén-Aulin, M''' (2003) fusB is an allele of nadD, encoding nicotinate mononucleotide adenylyltransferase in Escherichia coli.''Microbiology (Reading, Engl.)'' '''149''':2427-33

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Isolation of the temperature-sensitive Escherichia coli mutant 72c has been described previously. The mutant allele was named fusB and causes a pleiotropic phenotype, the most striking features of which, besides temperature sensitivity, are the inability to grow on synthetic medium and supersensitivity to trimethoprim, an antibiotic that inhibits the C1 metabolism. This work shows that the fusB mutation is a frameshift mutation in the nadD gene that encodes nicotinate mononucleotide adenylyltransferase. The frameshift leads to a change of the last 10 amino acids and an addition of 17 amino acids. This lesion, renamed nadD72, leads to very little NAD+ and NADPH synthesis at the permissive temperature and essentially no synthesis at the non-permissive temperature. As a comparison, a new mutation in the nadD gene, with an amino acid change in the ATP-binding site, has been isolated. Its NAD+ synthesis is decreased at 30 degrees C but the level is still sufficient to support normal growth. At 42 degrees C, NAD+ synthesis is reduced further, which leads to temperature sensitivity on minimal medium. This mutation was designated nadD74. Thus, a small decrease in NAD+ levels affects ability to grow on minimal medium at 42 degrees C, while a large decrease leads to a more pleiotropic phenotype.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12949168 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228435'
|- {{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.Q47a9ccf84b646&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:14611652

2008-02-06T15:06:28Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Voit, EO and Riley, M''' (2003) Extending knowledge of Escherichia coli metabolism by modeling and experiment.''Genome Biol.'' '''4''':235

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || One of the challenges for 'post-genomic' biology is the integration of data from many different sources. Two recent studies independently take steps towards this goal for Escherichia coli, using mathematical modeling and a combination of gene expression and protein levels to predict new gene functions and metabolic behaviors.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14611652 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228434'
|- {{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.V47a9ccf382035&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12823825

2008-02-06T15:06:22Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Yates, J, Aroyo, M, Sherratt, DJ and Barre, FX''' (2003) Species specificity in the activation of Xer recombination at dif by FtsK.''Mol. Microbiol.'' '''49''':241-9

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || In Escherichia coli, chromosome dimers are resolved to monomers by the addition of a single cross-over at a specific locus on the chromosome, dif. Recombination is performed by two tyrosine recombinases, XerC and XerD, and requires the action of an additional protein, FtsK. We show that Haemophilus influenzae FtsK activates recombination by H. influenzae XerCD at H. influenzae dif. However, it cannot activate recombination by E. coli XerCD. Reciprocally, E. coli FtsK cannot activate recombination by the H. influenzae recombinases at H. influenzae dif. We took advantage of this species specificity to gain further insight into the mechanism of activation of Xer recombination at dif by FtsK. We mapped the region of FtsK implicated in species specificity to the extreme 140-amino-acid C-terminal residues of the protein. Our results suggest that FtsK interacts directly with XerCD in order to activate recombination at dif.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12823825 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228433'
|- {{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.X47a9ccee24bd1&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12761291

2008-02-06T15:06:17Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Ando, T, Tanaka, T and Kikuchi, Y''' (2003) Substrate shape specificity of E coli RNase P ribozyme is dependent on the concentration of magnesium ion.''J. Biochem.'' '''133''':445-51

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || The bacterial RNase P ribozyme can accept a hairpin RNA with CCA-3' tag sequence as well as a cloverleaf pre-tRNA as substrate in vitro, but the details are not known. By switching tRNA structure using an antisense guide DNA technique, we examined the Escherichia coli RNase P ribozyme specificity for substrate RNA of a given shape. Analysis of the RNase P reaction with various concentrations of magnesium ion revealed that the ribozyme cleaved only the cloverleaf RNA at below 10 mM magnesium ion. At 10 mM magnesium ion or more, the ribozyme also cleaved a hairpin RNA with a CCA-3' tag sequence. At above 20 mM magnesium ion, cleavage site wobbling by the enzyme in tRNA-derived hairpin occurred, and the substrate specificity of the enzyme became broader. Additional studies using another hairpin substrate demonstrated the same tendency. Our data strongly suggest that raising the concentration of metal ion induces a conformational change in the RNA enzyme.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12761291 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228432'
|- {{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.O47a9cce95378e&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:14651631

2008-02-06T15:06:12Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Mora, L, Zavialov, A, Ehrenberg, M and Buckingham, RH''' (2003) Stop codon recognition and interactions with peptide release factor RF3 of truncated and chimeric RF1 and RF2 from Escherichia coli.''Mol. Microbiol.'' '''50''':1467-76

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Release factors RF1 and RF2 recognize stop codons present at the A-site of the ribosome and activate hydrolysis of peptidyl-tRNA to release the peptide chain. Interactions with RF3, a ribosome-dependent GTPase, then initiate a series of reactions that accelerate the dissociation of RF1 or RF2 and their recycling between ribosomes. Two regions of Escherichia coli RF1 and RF2 were identified previously as involved in stop codon recognition and peptidyl-tRNA hydrolysis. We show here that removing the N-terminal domain of RF1 or RF2 or exchanging this domain between the two factors does not affect RF specificity but has different effects on the activity of RF1 and RF2: truncated RF1 remains highly active and able to support rapid cell growth, whereas cells with truncated RF2 grow only poorly. Transplanting a loop of 13 amino acid residues from RF2 to RF1 switches the stop codon specificity. The interaction of the truncated factors with RF3 on the ribosome is defective: they fail to stimulate guanine nucleotide exchange on RF3, recycling is not stimulated by RF3, and nucleotide-free RF3 fails to stabilize the binding of RF1 or RF2 to the ribosome. However, the N-terminal domain seems not to be required for the expulsion of RF1 or RF2 by RF3:GTP.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14651631 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228431'
|- {{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.F47a9cce427751&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:14640699

2008-02-06T15:06:07Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Powl, AM, East, JM and Lee, AG''' (2003) Lipid-protein interactions studied by introduction of a tryptophan residue: the mechanosensitive channel MscL.''Biochemistry'' '''42''':14306-17

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Trp fluorescence spectroscopy is a powerful tool to study the structures of membrane proteins and their interactions with the surrounding lipid bilayer. Many membrane proteins contain more than one Trp residue, making analysis of the fluorescence data more complex. The mechanosensitive channels MscL's of Mycobacterium tuberculosis (TbMscL) and Escherichia coli (EcMscL) contain no Trp residues. We have therefore introduced single Trp residues into the transmembrane regions of TbMscL and EcMscL to give the Trp-containing mutants F80W-TbMscL and F93W-EcMscL, respectively, which we show are highly suitable for measurements of lipid binding constants. In vivo cell viability assays in E. coli show that introduction of the Trp residues does not block function of the channels. The Trp-containing mutants have been reconstituted into lipid bilayers by mixing in cholate followed by dilution to re-form membranes. Cross-linking experiments suggest that the proteins retain their pentameric structures in phosphatidylcholines with chain lengths between C14 and C24, phosphatidylserines, and phosphatidic acid. Quenching of Trp fluorescence by brominated phospholipids suggests that the Trp residue in F80W-TbMscL is more exposed to the lipid bilayer than the Trp residue in F93W-EcMscL. Binding constants for phosphatidylcholines change with changing fatty acyl chain length, the strongest interaction for both TbMscL and EcMscL being observed with a chain of length C16, corresponding to a bilayer of hydrophobic thickness ca. 24 A, compared to a hydrophobic thickness for TbMscL of about 26 A estimated from the crystal structure. Lipid binding constants change by only a factor of 1.5 in the chain length range from C12 to C24, much less than expected from theories of hydrophobic mismatch in which the protein is treated as a rigid body. It is concluded that MscL distorts to match changes in bilayer thickness. The binding constants for dioleoylphosphatidylethanolamine for both TbMscL and EcMscL relative to those for dioleoylphosphatidylcholine are close to 1. Quenching experiments suggest a single class of binding sites for phosphatidylserine, phosphatidylglycerol, and cardiolipin on TbMscL; binding constants are greater than those for phosphatidylcholine and decrease with increasing ionic strength, suggesting that charge interactions are important in binding these anionic phospholipids. Quenching experiments suggest two classes of lipid binding sites on TbMscL for phosphatidic acid, binding of phosphatidic acid being much less dependent on ionic strength than binding of phosphatidylserine.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14640699 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228430'
|- {{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.Q47a9ccde8761b&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12940820

2008-02-06T15:06:01Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Hishida, T, Iwasaki, H, Han, YW, Ohnishi, T and Shinagawa, H''' (2003) Uncoupling of the ATPase activity from the branch migration activity of RuvAB protein complexes containing both wild-type and ATPase-defective RuvB proteins.''Genes Cells'' '''8''':721-30

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || BACKGROUND: Escherichia coli RuvAB promotes branch migration of Holliday junctions during recombination repair and homologous recombination. RuvB forms a hexameric ring through which duplex DNA passes and is translocated in an ATP-dependent manner. ATPase-deficient RuvB mutant K68A has a mutation in the Walker A motif and exerts a dominant-negative effect on in vivo repair of UV-induced DNA damage. In this study, we examined RuvAB-dependent branch migration in the presence of a mutant RuvB, K68A. RESULTS: Mixing K68A with wild-type RuvB resulted in the formation of heterohexamers that showed unique properties of DNA binding, ATPase, and branch migration activities different from those of either wild-type or mutant homohexamers. RuvB heterohexamers inhibited branch migration and caused Holliday junctions to accumulate during RecA-mediated strand exchange. In the presence of RuvA, RuvB heterohexamers had Holliday junction-dependent ATPase activity, but did not promote branch migration. CONCLUSIONS: These results suggest that functional cooperation among the subunits in the hexamers is required for branch migration, but inclusion of inactive subunits is tolerated for ATP hydrolysis. Therefore, we propose that an essential ATP hydrolysis-dependent functional cooperation is induced in RuvB hexamer subunits during RuvAB-mediated branch migration.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12940820 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228429'
|- {{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.V47a9ccd826f65&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12829462

2008-02-06T15:05:55Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Grayson, P, Tajkhorshid, E and Schulten, K''' (2003) Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics.''Biophys. J.'' '''85''':36-48

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Interactive molecular dynamics, a new modeling tool for rapid investigation of the physical mechanisms of biological processes at the atomic level, is applied to study selectivity and regulation of the membrane channel protein GlpF and the enzyme glycerol kinase. These proteins facilitate the first two steps of Escherichia coli glycerol metabolism. Despite their different function and architecture the proteins are found to employ common mechanisms for substrate selectivity: an induced geometrical fit by structurally homologous binding sites and an induced rapid dipole moment reversal. Competition for hydrogen bonding sites with water in both proteins is critical for substrate motion. In glycerol kinase, it is shown that the proposed domain motion prevents competition with water, in turn regulating the binding of glycerol.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12829462 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228428'
|- {{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.Z47a9ccd31aeaf&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:14674763

2008-02-06T15:05:50Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Setterdahl, AT, Chivers, PT, Hirasawa, M, Lemaire, SD, Keryer, E, Miginiac-Maslow, M, Kim, SK, Mason, J, Jacquot, JP, Longbine, CC, de Lamotte-Guery, F and Knaff, DB''' (2003) Effect of pH on the oxidation-reduction properties of thioredoxins.''Biochemistry'' '''42''':14877-84

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Oxidation-reduction midpoint potential (E(m)) versus pH profiles were measured for wild-type thioredoxins from Escherichia coli and from the green alga Chlamydomonas reinhardtii and for a number of site-directed mutants of these two thioredoxins. These profiles all exhibit slopes of approximately -59 mV per pH unit, characteristic of the uptake of two protons per reduction of an active-site thioredoxin disulfide, at acidic, neutral, and moderately alkaline pH values. At higher pH values, these profiles exhibit slopes of either -29.5 mV per pH unit, characteristic of the uptake of one proton per disulfide reduced, or are pH-independent, indicating that neither proton uptake nor proton release is associated with reduction of the active-site disulfide. Reduction of the two wild-type thioredoxins is accompanied by the uptake of two protons even at pH values where the more acidic cysteine thiol group of the reduced proteins would be expected to be completely unprotonated. The effect of site-directed mutagenesis of two highly conserved aspartate residues that play important structural and/or catalytic roles in both thioredoxins, and which could in principle play a role in proton transfer, on the pK(a) values of redox-linked acid dissociations (deduced from changes in slope of the E(m) versus pH profiles) has also been determined for both E. coli thioredoxin and C. reinhardtii thioredoxin h.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14674763 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228427'
|- {{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.O47a9cccd84992&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12843673

2008-02-06T15:05:45Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''He, M, Nie, YF and Xu, P''' (2003) A T42M substitution in bacterial 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) generates enzymes with increased resistance to glyphosate.''Biosci. Biotechnol. Biochem.'' '''67''':1405-9

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Mutants of class I enolpyruvylshikimate 3-phosphate synthase (EPSPS) with resistance to glyphosate were produced in a previous study using the staggered extension process with aroA genes from S. typhimurium and E. coli. Two of these mutants shared a common amino acid substitution, T42M, near the hinge region between the large globular domains of EPSPS. Using site-directed mutagenisis, we produced the T42M mutants without the other amino acid changes of the original mutants. The T42M substitution alone produced enzymes with a 9- to 25-fold decreased K(m)[PEP] and a 21- to 26-fold increased K(i)[glyphosate] compared to the wild-type enzymes. These results provide more testimony for the powerful approach for protein engineering by the combination of directed evolution and rational design.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12843673 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228426'
|- {{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.Y47a9ccc8aecd8&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12829519

2008-02-06T15:05:39Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Pham, AS and Reinhart, GD''' (2003) Quantification of allosteric influence of Escherichia coli phosphofructokinase by frequency domain fluorescence.''Biophys. J.'' '''85''':656-66

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || The allosteric properties of the wild-type Escherichia coli phosphofructokinase were compared to the E187A mutant by using frequency-domain techniques. Tryptophan-shifted mutants comprising of double (W311Y/Y55W and W/311F/F188W) and triple (W311Y/Y55W/E187A and W311F/F188W/E187A) amino acid residue changes, which allowed for better fluorescence probing at targeted sites, were also compared to the wild-type and E187A. The additive nature of multiple mutations allowed one to partition the net effect of modifying residue 187. In general, the mutant enzymes displayed greater heterogeneity in sub-state population than did the wild-type enzyme. The semi-cone angle model was used to quantify the extent of depolarization of the fluorophore. Use of the model presupposes that the extent of depolarization directly correlates with the degree of flexibility of the fluorophore. A relationship has been established between the values determined from the semi-cone angle calculations and the thermodynamic components responsible for the allosteric linkage between the regulatory and substrate binding. Coupling interactions giving rise to positive entropy components are manifested by increasing flexibility of the ternary complexes rather than the binary complexes.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12829519 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228425'
|- {{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.V47a9ccc317e6d&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:13678294

2008-02-06T15:05:34Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Ravanal, MC, Goldie, H and Cardemil, E''' (2003) Thermal stability of phosphoenolpyruvate carboxykinases from Escherichia coli, Trypanosoma brucei, and Saccharomyces cerevisiae.''J. Protein Chem.'' '''22''':311-5

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || The quaternary structure of ATP-dependent phosphoenolpyruvate (PEP) carboxykinases is variable. Thus, the carboxykinases from Escherichia coli, Trypanosoma brucei, and Saccharomyces cerevisiae are monomer, homodimer, and homotetramer, respectively. In this work, we studied the effect of temperature on the stability of the enzyme activity of these three carboxykinases, and have found that it follows the order monomer > dimer > tetramer. The inactivation processes are first order with respect to active enzyme. The presence of substrates leads to an increase in the thermal stability of all three PEP carboxykinases. The protection effect of the substrates on the thermal inactivation of these enzymes suggests similarities in the substrate-bound form of these proteins. We propose that the higher structural complexity of some PEP carboxykinases could be related to the acquisition of properties of relevance in vivo.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=13678294 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228424'
|- {{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.C47a9ccbe4828f&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12898065

2008-02-06T15:05:29Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Steiner, P and Sauer, U''' (2003) Overexpression of the ATP-dependent helicase RecG improves resistance to weak organic acids in Escherichia coli.''Appl. Microbiol. Biotechnol.'' '''63''':293-9

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || Increased resistance to several weak organic acids was conferred on Escherichia coli by overexpression of the ATP-dependent helicase RecG and, to a lesser extent, by overexpressing the helicase RuvAB. This property of helicases was identified by reproducible selection of recG-bearing clones from genomic libraries of the acetate-resistant species Acetobacter aceti and Staphylococcus capitis. We show that overexpression of RecG from both species, but also from E. coli, increased the maximum biomass concentration attained by E. coli cultures that were grown in the presence of various weak organic acids and uncouplers. Furthermore, overexpression of RecG from A. aceti significantly improved the maximum growth rates of E. coli under weak organic acid challenge. Based on the known role of RecG in DNA replication/repair, our data provide a first indication that weak organic acids negatively affect DNA replication and/or repair, and that these negative effects may be counteracted by helicase activity.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12898065 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228423'
|- {{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.D47a9ccb8a4b9c&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:14622424

2008-02-06T15:05:24Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Stewart, V, Chen, LL and Wu, HC''' (2003) Response to culture aeration mediated by the nitrate and nitrite sensor NarQ of Escherichia coli K-12.''Mol. Microbiol.'' '''50''':1391-9

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || Respiratory enzyme synthesis in enterobacteria is controlled in response to electron acceptor availability. The iron-sulphur protein Fnr and the sensor-regulator proteins ArcB-ArcA control respiratory gene transcription in response to oxygen and quinone pool redox status respectively. The sensor-regulator proteins NarX-NarL and NarQ-NarP control anaerobic respiratory gene expression in response to nitrate and nitrite. Our laboratory recently engineered the lac operon to replace the primary operator O1-lac with the NarL and NarP protein binding site from the nirB operon. Expression of the lacZ gene from this construct is repressed by nitrate in Nar+ strains. Here, we found that lacZ gene expression was repressed in aerated cultures of narQ+narX null strains. This repression was not observed in narX+narQ+ or narX+narQ null strains. Thus, the NarQ sensor responds to aeration as well as to nitrate and nitrite. The NarX and NarQ sensors are composed of three distinct modules: an amino-terminal sensory module, a carboxyl-terminal transmitter module and a central module of unknown function. Experiments with NarX-NarQ hybrid proteins suggest that the NarQ protein central module is necessary for response to aeration. The physiological significance of this additional sensory role for the NarQ sensor remains obscure.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14622424 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228422'
|- {{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.T47a9ccb388d3e&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:14671322

2008-02-06T15:05:18Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Stokes, NR, Murray, HD, Subramaniam, C, Gourse, RL, Louis, P, Bartlett, W, Miller, S and Booth, IR''' (2003) A role for mechanosensitive channels in survival of stationary phase: regulation of channel expression by RpoS.''Proc. Natl. Acad. Sci. U.S.A.'' '''100''':15959-64

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || The mechanosensitive (MS) channels MscS and MscL are essential for the survival of hypoosmotic shock by Escherichia coli cells. We demonstrate that MscS and MscL are induced by osmotic stress and by entry into stationary phase. Reduced levels of MS proteins and reduced expression of mscL- and mscS-LacZ fusions in an rpoS mutant strain suggested that the RNA polymerase holoenzyme containing sigmaS is responsible, at least in part, for regulating production of MS channel proteins. Consistent with the model that the effect of sigmaS is direct, the MscS and MscL promoters both use RNA polymerase containing sigmaS in vitro. Conversely, clpP or rssB mutations, which cause enhanced levels of sigmaS, show increased MS channel protein synthesis. RpoS null mutants are sensitive to hypoosmotic shock upon entry into stationary phase. These data suggest that MscS and MscL are components of the RpoS regulon and play an important role in ensuring structural integrity in stationary phase bacteria.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14671322 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228421'
|- {{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.R47a9ccae317a7&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12951767

2008-02-06T15:05:13Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Griffith, M and Gietz, RD''' (2003) Escherichia coli endA deletion strain for use in two-hybrid shuttle vector selection.''BioTechniques'' '''35''':272-4, 276, 278

{|{{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=12951767 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228420'
|- {{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.C47a9cca9420da&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12951523

2008-02-06T15:05:09Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Ando, T, Tanaka, T and Kikuchi, Y''' (2003) Comparative analyses of hairpin substrate recognition by Escherichia coli and Bacillus subtilis ribonuclease P ribozymes.''Biosci. Biotechnol. Biochem.'' '''67''':1825-7

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || Previously, we reported that the substrate shape recognition of the Escherichia coli ribonuclease (RNase) P ribozyme depends on the concentration of magnesium ion in vitro. We additionally examined the Bacillus subtilis RNase P ribozyme and found that the B. subtilis enzyme also required high magnesium ion, above 10 mM, for cleavage of a hairpin substrate. The results of kinetic studies showed that the metal ion concentration affected both the catalysis and the affinity of the ribozymes toward a hairpin RNA substrate.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12951523 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228419'
|- {{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.M47a9cca46e573&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:14602898

2008-02-06T15:05:03Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Chambers, AL, Smith, AJ and Savery, NJ''' (2003) A DNA translocation motif in the bacterial transcription--repair coupling factor, Mfd.''Nucleic Acids Res.'' '''31''':6409-18

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || The bacterial transcription-repair coupling factor, Mfd, is a superfamily II helicase that releases transcription elongation complexes stalled by DNA damage or other obstacles. Transcription complex displacement is an ATP-dependent reaction that is thought to involve DNA translocation without the strand separation associated with classical helicase activity. We have identified single amino acid substitutions within Mfd that disrupt the ability of Mfd to displace RNA polymerase but do not prevent ATP hydrolysis or binding to DNA. These substitutions, or deletion of the C-terminal 209 residues of Mfd, abrogate the ability of Mfd to increase the efficiency of roadblock repression in vivo. The substitutions fall in a region of Mfd that is homologous to the 'TRG' motif of RecG, a protein that catalyses ATP-dependent translocation of Holliday junctions. Our results define a translocation motif in Mfd and suggest that Mfd and RecG couple ATP hydrolysis to translocation of DNA in a similar manner.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14602898 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228418'
|- {{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.T47a9cc9f0d956&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12915732

2008-02-06T15:04:58Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Tsumoto, K, Umetsu, M, Yamada, H, Ito, T, Misawa, S and Kumagai, I''' (2003) Immobilized oxidoreductase as an additive for refolding inclusion bodies: application to antibody fragments.''Protein Eng.'' '''16''':535-41

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Three foldases--the apical domain of GroEL (mini-chaperone) and two oxidoreductases (DsbA and DsbC) from Escherichia coli--were studied in refolding a protein with immunoglobulin fold (immunoglobulin-folded protein) that had been produced as inclusion bodies in E.coli. The foldases promoted the refolding of single-chain antibody fragments from denaturant-solubilized and reduced inclusion bodies in vitro, and also effectively functioned as alternatives for labilizing agent and oxidizing reagent in the stepwise dialysis system. Immobilization of the oxidoreductases enhanced refolding and recovery of functional single-chain antibody in the dialysis system, suggesting that immobilized oxidoreductases can be used as an effective additive for refolding immunoglobulin-folded proteins in vitro.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12915732 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228417'
|- {{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.W47a9cc9a0ce43&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12889023

2008-02-06T15:04:53Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Engel, S, Vyazmensky, M, Geresh, S, Barak, Z and Chipman, DM''' (2003) Acetohydroxyacid synthase: a new enzyme for chiral synthesis of R-phenylacetylcarbinol.''Biotechnol. Bioeng.'' '''83''':833-40

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || We have found that acetohydroxyacid synthase (AHAS) is an efficient catalyst for the enantiospecific (> or =98% enantiomeric excess) synthesis of (R)-phenylacetylcarbinol (R-PAC) from pyruvate and benzaldehyde, despite the fact that its normal physiological role is synthesis of (S)-acetohydroxyacids from pyruvate and a second ketoacid. (R)-phenylacetylcarbinol is the precursor of important drugs having alpha and beta adrenergic properties, such as L-ephedrine, pseudoephedrine, and norephedrin. It is currently produced by whole-cell fermentations, but the use of the isolated enzyme pyruvate decarboxylase (PDC) for this purpose is the subject of active research and development efforts. Some of the AHAS isozymes of Escherichia coli have important advantages compared to PDC, including negligible acetaldehyde formation and high conversion of substrates (both pyruvate and benzaldehyde) to PAC. Acetohydroxyacid synthase isozyme I is particularly efficient. The reaction is not limited to condensation of pyruvate with benzaldehyde and other aromatic aldehydes may be used.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12889023 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228416'
|- {{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.W47a9cc950a548&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12944258

2008-02-06T15:04:48Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Faraldo-Gómez, JD, Smith, GR and Sansom, MS''' (2003) Molecular dynamics simulations of the bacterial outer membrane protein FhuA: a comparative study of the ferrichrome-free and bound states.''Biophys. J.'' '''85''':1406-20

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || FhuA is one of the more complex members of the superfamily of bacterial outer membrane proteins. Its primary function is to provide a binding site on the outer membrane surface for siderophores, such as ferrichrome, and subsequently to facilitate their energy-dependent transport across the membrane, presumably powered by the TonB-ExbBD protein complex that resides in the cytoplasmic membrane. Crystal structures of FhuA with and without a bound ferrichrome molecule have provided some clues as to the initial stages of the siderophore transport mechanism. In the current study, we have employed 10-ns duration molecular dynamics simulations of FhuA and of the FhuA-ferrichrome complex, both embedded in a phospholipid bilayer, to probe the short timescale dynamics of this integral membrane protein, and to explore possible mechanistic implications of this dynamic behavior. Analysis of the dynamics of the protein suggests that the extracellular loops move as relatively rigid entities relative to the transmembrane beta-barrel. Comparison of the two simulations (with and without bound ferrichrome) revealed some ligand-induced changes in loop mobility. Specifically, loop L8 appears to be involved in a mechanism whereby the binding site is gated closed upon ligand binding. Analysis of the dynamics of water molecules within the core of the FhuA protein provided no evidence for a water-permeable protopore through which the ferrichrome might pass without a major perturbation of the FhuA protein. Overall, these simulations support the proposal that binding of ferrichrome initiates a signaling mechanism that ultimately leads to the TonB-mediated partial or total removal of the core domain from the beta-barrel, thus opening up a permeable pore. These simulations are among the longest that have been performed on a complex membrane protein. However, a simple analysis of sampling reveals that the description of protein motions is far from complete.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12944258 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228415'
|- {{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.E47a9cc8f5b88a&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:10987918

2008-02-06T12:02:06Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Sundaram, AK and Woodard, RW''' (2000) Probing the stereochemistry of E. coli 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (phenylalanine-sensitive)-catalyzed synthesis of KDO 8-P analogues.''J. Org. Chem.'' '''65''':5891-7

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || The five-carbon phosphorylated monosaccharide analogues, D-arabinose 5-phosphate, D-ribose 5-phosphate, and 2-deoxy-D-ribose 5-phosphate, were separately condensed with (Z)- and (E)-[3-(2)H]-phosphoenolpyruvate (PEP) in the presence of Escherichia coli 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAH 7-P) synthase (phe) to give in the case of (Z)-[3-(2)H]-PEP (3S)-[3-(2)H]-3-deoxy-D-manno-octulosonate 8-phosphate, (3S)-[3-(2)H]-3-deoxy-D-altro-octulosonate 8-phosphate, and (3S)-[3-(2)H]-3,5-dideoxy-D-altro-octulosonate 8-phosphate, respectively, whereas incubation with (E)-[3-(2)H]-PEP gives the corresponding (3R)-monosaccharides. These results are in complete agreement with the observed facial selectivity of DAH 7-P synthase for its normal substrates D-erythrose 4-phosphate and PEP and provide direct evidence that DAH 7-P synthase (phe) catalyzes the si face addition of the C3 of PEP to the re face of C1 of the phosphorylated monosaccharides tested. Products formed by DAH 7-P synthase (phe)-catalyzed condensation of (Z)- and (E)-[3-F]-PEP with E 4-P were completely characterized by (1)H and (19)F NMR analysis for the first time. Results of our studies suggest that disappearence of the double bond between C2 and C3 of PEP and formation of a bond between C3 of PEP and C1 of the phosphorylated monosaccharide tested occur in concert during the DAH 7-P synthase-catalyzed condensation reaction.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10987918 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='228412'
|- {{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.I47a9a1be055c4&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:10995235

2008-02-06T12:02:00Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Spudich, G and Marqusee, S''' (2000) A change in the apparent m value reveals a populated intermediate under equilibrium conditions in Escherichia coli ribonuclease HI.''Biochemistry'' '''39''':11677-83

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Experimental studies of protein stability often rely on the determination of an "m value", which describes the denaturant dependence of the free energy change between two states (DeltaG = DeltaG(H2O) - m[denaturant]). Changes in the m value accompanying site specific mutations are usually attributed to structural alterations in the native or unfolded ensemble. Here, we provide an example of significant reduction in the m value resulting from a subtle deviation in two-state behavior not detected by traditional methods. The protein that is studied is a variant of Escherchia coli RNase H in which three residues predicted to be involved in a partially buried salt bridge network were mutated to alanine (R46A, D102A, and D148A). Equilibrium denaturant profiles monitored by both fluorescence and circular dichroism appeared to be cooperative, and a two-state analysis yielded a DeltaG(UN) of approximately -3 kcal/mol with an m value of 1.4 kcal mol(-1) M(-1) (vs 2.3 for RNase H). Analysis of kinetic refolding experiments suggests that the system is actually three-state at equilibrium with an appreciable concentration of an intermediate state under low denaturant concentrations. The stability of the native state determined from a fit of these kinetic data is -6.7 kcal/mol, suggesting that the stability determined by traditional two-state equilibrium analysis is a gross underestimate. The only hint to this loss of two-state behavior was a decrease in the apparent m value, and the presence of the equilibrium intermediate was only identified by a kinetic analysis. Our work serves as a cautionary note; the possibility of a three-state system should be closely addressed before interpreting a change in the m value as a change in the native or unfolded state.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10995235 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
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<protect>

{|class = 'sortable' {{Prettytable}} id='228411'
|- {{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.G47a9a1b7c3db1&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

PMID:10986237

2008-02-06T12:01:54Z

172.16.48.28: New PMID: Page!

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{{RightTOC}}

 '''Sprencel, C, Cao, Z, Qi, Z, Scott, DC, Montague, MA, Ivanoff, N, Xu, J, Raymond, KM, Newton, SM and Klebba, PE''' (2000) Binding of ferric enterobactin by the Escherichia coli periplasmic protein FepB.''J. Bacteriol.'' '''182''':5359-64

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || The periplasmic protein FepB of Escherichia coli is a component of the ferric enterobactin transport system. We overexpressed and purified the binding protein 23-fold from periplasmic extracts by ammonium sulfate precipitation and chromatographic methods, with a yield of 20%, to a final specific activity of 15,500 pmol of ferric enterobactin bound/mg. Periplasmic fluid from cells overexpressing the binding protein adsorbed catecholate ferric siderophores with high affinity: in a gel filtration chromatography assay the K(d) of the ferric enterobactin-FepB binding reaction was approximately 135 nM. Intrinsic fluorescence measurements of binding by the purified protein, which were more accurate, showed higher affinity for both ferric enterobactin (K(d) = 30 nM) and ferric enantioenterobactin (K(d) = 15 nM), the left-handed stereoisomer of the natural E. coli siderophore. Purified FepB also adsorbed the apo-siderophore, enterobactin, with comparable affinity (K(d) = 60 nM) but did not bind ferric agrobactin. Polyclonal rabbit antisera and mouse monoclonal antibodies raised against nearly homogeneous preparations of FepB specifically recognized it in solid-phase immunoassays. These sera enabled the measurement of the FepB concentration in vivo when expressed from the chromosome (4,000 copies/cell) or from multicopy plasmids (>100,000 copies/cell). Overexpression of the binding protein did not enhance the overall affinity or rate of ferric enterobactin transport, supporting the conclusion that the rate-limiting step of ferric siderophore uptake through the cell envelope is passage through the outer membrane.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10986237 PubMed]
|}
</protect>
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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='228410'
|- {{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.A47a9a1b202e90&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
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PMID:10954591

2008-02-06T12:01:49Z

172.16.48.28: New PMID: Page!

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 '''Shimokawa, H, Fujii, Y, Furuichi, M, Sekiguchi, M and Nakabeppu, Y''' (2000) Functional significance of conserved residues in the phosphohydrolase module of Escherichia coli MutT protein.''Nucleic Acids Res.'' '''28''':3240-9

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|{{TableHeadingColor}} |'''Abstract''' || Escherichia coli MutT protein hydrolyzes 8-oxo-7,8-dihydro-2'-dGTP (8-oxo-dGTP) to the monophosphate, thus avoiding the incorporation of 8-oxo-7,8-dihydroguanine (8-oxo-G) into nascent DNA. Bacterial and mammalian homologs of MutT protein share the phosphohydrolase module (MutT: Gly37-->Gly59). By saturation mutagenesis of conserved residues in the MutT module, four of the 10 conserved residues (Gly37, Gly38, Glu53 and Glu57) were revealed to be essential to suppress spontaneous A:T-->C:G transversion mutation in a mutT(-) mutator strain. For the other six residues (Lys39, Glu44, Thr45, Arg52, Glu56 and Gly59), many positive mutants which can suppress the spontaneous mutation were obtained; however, all of the positive mutants for Glu44 and Arg52 either partially or inefficiently suppressed the mutation, indicating that these two residues are also important for MutT function. Several positive mutants for Lys39, Thr45, Glu56 and Gly59 efficiently decreased the elevated spontaneous mutation rate, as seen with the wild-type, hence, these four residues are non-essential for MutT function. As Lys38 and Glu55 in human MTH1, corresponding to the non-essential residues Lys39 and Glu56 in MutT, could not be replaced by any other residue without loss of function, different structural features between the two modules of MTH1 and MutT proteins are evident.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10954591 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='228409'
|- {{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.N47a9a1acee4ab&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
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PMID:11009612

2008-02-06T12:01:44Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Sha, R, Iwasaki, H, Liu, F, Shinagawa, H and Seeman, NC''' (2000) Cleavage of symmetric immobile DNA junctions by Escherichia coli RuvC.''Biochemistry'' '''39''':11982-8

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|{{TableHeadingColor}} |'''Abstract''' || The Holliday junction is a key DNA intermediate in the process of genetic recombination. It consists of two double-helical domains composed of homologous strands that flank a branch point; two of the strands are roughly helical, and two form the crossover between the helices. RuvC is a Holliday junction resolvase that cleaves the helical strands at a symmetric sequence, leading to the production of two recombinant molecules. We have determined the position of the cleavage site relative to the crossover point by the use of symmetric immobile junctions; these are DNA molecules containing two crossover points, one held immobile by sequence asymmetry and the second a symmetric sequence, but held immobile by torsional coupling to the first junction. We have built five symmetric immobile junctions, in which the tetranucleotide recognition site is moved stepwise relative to the branch point. We have used kinetic analysis of catalysis, gel retardation, and hydroxyl radical hypersensitivity to analyze this system. We conclude that the internucleotide linkage one position 3' to the crossover point is the favored site of cleavage.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11009612 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='228408'
|- {{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.D47a9a1a78c397&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
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PMID:10972842

2008-02-06T12:01:39Z

172.16.48.28: New PMID: Page!

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 '''Seitz, H, Weigel, C and Messer, W''' (2000) The interaction domains of the DnaA and DnaB replication proteins of Escherichia coli.''Mol. Microbiol.'' '''37''':1270-9

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || The initiation of chromosome replication in Escherichia coli requires the recruitment of the replicative helicase DnaB from the DnaBC complex to the unwound region within the replication origin oriC, supported by the oriC-bound initiator protein DnaA. We defined physical contacts between DnaA and DnaB that involve residues 24-86 and 130-148 of DnaA and residues 154-210 and 1-156 of DnaB respectively. We propose that contacts between DnaA and DnaB occur via two interaction sites on each of the proteins. Interaction domain 24-86 of DnaA overlaps with its N-terminal homo-oligomerization domain (residues 1-86). Interaction domain 154-210 of DnaB overlaps or is contiguous with the domains known to interact with plasmid initiator proteins. Loading of the DnaBC helicase in vivo can only be performed by DnaA derivatives containing (in addition to residues 24-86 and the DNA-binding domain 4) a structurally intact domain 3. Nucleotide binding by domain 3 is, however, not required. The parts of DnaA required for replication of pSC101 were clearly different from those used for helicase loading. Domains 1 and 4 of DnaA, but not domain 3, were found to be involved in the maintenance of plasmid pSC101.
</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=10972842 PubMed]
|}
</protect>
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<protect>

{|class = 'sortable' {{Prettytable}} id='228407'
|- {{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.P47a9a1a257b46&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
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<references/>

PMID:11032794

2008-02-06T12:01:33Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Unligil, UM, Zhou, S, Yuwaraj, S, Sarkar, M, Schachter, H and Rini, JM''' (2000) X-ray crystal structure of rabbit N-acetylglucosaminyltransferase I: catalytic mechanism and a new protein superfamily.''EMBO J.'' '''19''':5269-80

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || N:-acetylglucosaminyltransferase I (GnT I) serves as the gateway from oligomannose to hybrid and complex N:-glycans and plays a critical role in mammalian development and possibly all metazoans. We have determined the X-ray crystal structure of the catalytic fragment of GnT I in the absence and presence of bound UDP-GlcNAc/Mn(2+) at 1.5 and 1.8 A resolution, respectively. The structures identify residues critical for substrate binding and catalysis and provide evidence for similarity, at the mechanistic level, to the deglycosylation step of retaining beta-glycosidases. The structuring of a 13 residue loop, resulting from UDP-GlcNAc/Mn(2+) binding, provides an explanation for the ordered sequential 'Bi Bi' kinetics shown by GnT I. Analysis reveals a domain shared with Bacillus subtilis glycosyltransferase SpsA, bovine beta-1,4-galactosyl transferase 1 and Escherichia coli N:-acetylglucosamine-1-phosphate uridyltransferase. The low sequence identity, conserved fold and related functional features shown by this domain define a superfamily whose members probably share a common ancestor. Sequence analysis and protein threading show that the domain is represented in proteins from several glycosyltransferase families.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11032794 PubMed]
|}
</protect>
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<protect>

{|class = 'sortable' {{Prettytable}} id='228406'
|- {{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.W47a9a19cbafc5&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
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PMID:11042447

2008-02-06T12:01:28Z

172.16.48.28: New PMID: Page!

<protect>
{{RightTOC}}

 '''Unligil, UM and Rini, JM''' (2000) Glycosyltransferase structure and mechanism.''Curr. Opin. Struct. Biol.'' '''10''':510-7

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || The high-resolution X-ray crystal structures of a new form of bacteriophage T4 beta-glucosyltransferase, Escherichia coli MurG, Bacillus subtilis SpsA, bovine beta-1,4-galactosyltransferase 1 and rabbit N-acetylglucosaminyltransferase I have now been solved. These glycosyltransferase structures have provided the first detailed view of the structural basis of catalysis, as well as new insight into glycosyltransferase classification.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11042447 PubMed]
|}
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==Significance {{HelpIcon|Help:Literature}} ==
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<protect>

{|class = 'sortable' {{Prettytable}} id='228405'
|- {{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.T47a9a197e62e5&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
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