EcoliWiki - User contributions [en]

Category:GO:0033554 ! cellular response to stress

2011-10-07T00:25:23Z

192.31.21.150: New GO term category page

{{GO term stub|GO:0033554_!_cellular_response_to_stress}}

==References==
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PMID:11752262

2011-04-02T07:26:43Z

192.31.21.150: Fill PMID: Page!

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<protect>
 '''Bahl, A, Brunk, B, Coppel, RL, Crabtree, J, Diskin, SJ, Fraunholz, MJ, Grant, GR, Gupta, D, Huestis, RL, Kissinger, JC, Labo, P, Li, L, McWeeney, SK, Milgram, AJ, Roos, DS, Schug, J and Stoeckert, CJ''' (2002) PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished).''Nucleic Acids Res.'' '''30''':87-90

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|{{TableHeadingColor}} |'''Abstract''' || <protect>PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates finished and draft genome sequence data and annotation emerging from Plasmodium sequencing projects. PlasmoDB currently houses information from five parasite species and provides tools for cross-species comparisons. Sequence information is also integrated with other genomic-scale data emerging from the Plasmodium research community, including gene expression analysis from EST, SAGE and microarray projects. The relational schemas used to build PlasmoDB [Genomics Unified Schema (GUS) and RNA Abundance Database (RAD)] employ a highly structured format to accommodate the diverse data types generated by sequence and expression projects. A variety of tools allow researchers to formulate complex, biologically based queries of the database. A version of the database is also available on CD-ROM (Plasmodium GenePlot), facilitating access to the data in situations where Internet access is difficult (e.g. by malaria researchers working in the field). The goal of PlasmoDB is to enhance utilization of the vast quantities of data emerging from genome-scale projects by the global malaria research community.</protect>
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|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11752262 PubMed]

|}
</protect>
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{{LitMaterials}}

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{| id="U4d96cfb3263b3" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177521.U4d96cfb3263b3&page=177521&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
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==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

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==References==
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PMID:11752262

2011-04-02T07:26:39Z

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PMID:12519984

2011-04-02T07:11:27Z

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<protect>
 '''Bahl, A, Brunk, B, Crabtree, J, Fraunholz, MJ, Gajria, B, Grant, GR, Ginsburg, H, Gupta, D, Kissinger, JC, Labo, P, Li, L, Mailman, MD, Milgram, AJ, Pearson, DS, Roos, DS, Schug, J, Stoeckert, CJ and Whetzel, P''' (2003) PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data.''Nucleic Acids Res.'' '''31''':212-5

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || <protect>PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates the recently completed P. falciparum genome sequence and annotation, as well as draft sequence and annotation emerging from other Plasmodium sequencing projects. PlasmoDB currently houses information from five parasite species and provides tools for intra- and inter-species comparisons. Sequence information is integrated with other genomic-scale data emerging from the Plasmodium research community, including gene expression analysis from EST, SAGE and microarray projects and proteomics studies. The relational schema used to build PlasmoDB, GUS (Genomics Unified Schema) employs a highly structured format to accommodate the diverse data types generated by sequence and expression projects. A variety of tools allow researchers to formulate complex, biologically-based, queries of the database. A stand-alone version of the database is also available on CD-ROM (P. falciparum GenePlot), facilitating access to the data in situations where internet access is difficult (e.g. by malaria researchers working in the field). The goal of PlasmoDB is to facilitate utilization of the vast quantities of genomic-scale data produced by the global malaria research community. The software used to develop PlasmoDB has been used to create a second Apicomplexan parasite genome database, ToxoDB (http://ToxoDB.org).</protect>
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|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12519984 PubMed]

|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
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{{LitMaterials}}

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<protect>

{| id="Y4d96cc1f75f6a" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177520.Y4d96cc1f75f6a&page=177520&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
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</protect>

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

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==References==
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PMID:12519984

2011-04-02T07:11:24Z

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PMID:18824479

2011-04-02T06:56:10Z

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<protect>
 '''Aurrecoechea, C, Brestelli, J, Brunk, BP, Carlton, JM, Dommer, J, Fischer, S, Gajria, B, Gao, X, Gingle, A, Grant, G, Harb, OS, Heiges, M, Innamorato, F, Iodice, J, Kissinger, JC, Kraemer, E, Li, W, Miller, JA, Morrison, HG, Nayak, V, Pennington, C, Pinney, DF, Roos, DS, Ross, C, Stoeckert, CJ, Sullivan, S, Treatman, C and Wang, H''' (2009) GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis.''Nucleic Acids Res.'' '''37''':D526-30

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|{{TableHeadingColor}} |'''Abstract''' || <protect>GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB (http://EuPathDB.org) family of functional genomic databases. GiardiaDB and TrichDB employ the same framework as other EuPathDB sites (CryptoDB, PlasmoDB and ToxoDB), supporting fully integrated and searchable databases. Genomic-scale data available via these resources may be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs and other protein characteristics. Functional queries may also be formulated, based on transcript and protein expression data from a variety of platforms. Phylogenetic relationships may also be interrogated. The ability to combine the results from independent queries, and to store queries and query results for future use facilitates complex, genome-wide mining of functional genomic data.</protect>
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|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18824479 PubMed]
Online version:[http://dx.doi.org/10.1093/nar/gkn631 10.1093/nar/gkn631]
|}
</protect>
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<protect>

{| id="A4d96c8891d5a2" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177519.A4d96c8891d5a2&page=177519&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
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{{LitLinks}}

==See also==

==References==
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PMID:18824479

2011-04-02T06:56:04Z

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PMID:12519989

2011-04-02T05:57:52Z

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<protect>
 '''Kissinger, JC, Gajria, B, Li, L, Paulsen, IT and Roos, DS''' (2003) ToxoDB: accessing the Toxoplasma gondii genome.''Nucleic Acids Res.'' '''31''':234-6

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|{{TableHeadingColor}} |'''Abstract''' || <protect>ToxoDB (http://ToxoDB.org) provides a genome resource for the protozoan parasite Toxoplasma gondii. Several sequencing projects devoted to T. gondii have been completed or are in progress: an EST project (http://genome.wustl.edu/est/index.php?toxoplasma=1), a BAC clone end-sequencing project (http://www.sanger.ac.uk/Projects/T_gondii/) and an 8X random shotgun genomic sequencing project (http://www.tigr.org/tdb/e2k1/tga1/). ToxoDB was designed to provide a central point of access for all available T. gondii data, and a variety of data mining tools useful for the analysis of unfinished, un-annotated draft sequence during the early phases of the genome project. In later stages, as more and different types of data become available (microarray, proteomic, SNP, QTL, etc.) the database will provide an integrated data analysis platform facilitating user-defined queries across the different data types.</protect>
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|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12519989 PubMed]

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

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{{LitMaterials}}

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

{| id="D4d96bae002f4a" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177518.D4d96bae002f4a&page=177518&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
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==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

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==References==
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PMID:12519989

2011-04-02T05:57:51Z

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PMID:18957442

2011-04-02T05:17:32Z

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<protect>
 '''Aurrecoechea, C, Brestelli, J, Brunk, BP, Dommer, J, Fischer, S, Gajria, B, Gao, X, Gingle, A, Grant, G, Harb, OS, Heiges, M, Innamorato, F, Iodice, J, Kissinger, JC, Kraemer, E, Li, W, Miller, JA, Nayak, V, Pennington, C, Pinney, DF, Roos, DS, Ross, C, Stoeckert, CJ, Treatman, C and Wang, H''' (2009) PlasmoDB: a functional genomic database for malaria parasites.''Nucleic Acids Res.'' '''37''':D539-43

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || <protect>PlasmoDB (http://PlasmoDB.org) is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB belongs to a family of genomic resources that are housed under the EuPathDB (http://EuPathDB.org) Bioinformatics Resource Center (BRC) umbrella. The latest release, PlasmoDB 5.5, contains numerous new data types from several broad categories--annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution. Data in PlasmoDB can be queried by selecting the data of interest from a query grid or drop down menus. Various results can then be combined with each other on the query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.</protect>
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|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18957442 PubMed]
Online version:[http://dx.doi.org/10.1093/nar/gkn814 10.1093/nar/gkn814]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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

{| id="P4d96b16c7cf5a" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177517.P4d96b16c7cf5a&page=177517&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
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==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
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PMID:18957442

2011-04-02T05:17:32Z

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PMID:17098930

2011-04-02T05:10:58Z

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<protect>
 '''Aurrecoechea, C, Heiges, M, Wang, H, Wang, Z, Fischer, S, Rhodes, P, Miller, J, Kraemer, E, Stoeckert, CJ, Roos, DS and Kissinger, JC''' (2007) ApiDB: integrated resources for the apicomplexan bioinformatics resource center.''Nucleic Acids Res.'' '''35''':D427-30

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|{{TableHeadingColor}} |'''Abstract''' || <protect>ApiDB (http://ApiDB.org) represents a unified entry point for the NIH-funded Apicomplexan Bioinformatics Resource Center (BRC) that integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises numerous veterinary and medically important parasitic protozoa including human pathogenic species of the genera Cryptosporidium, Plasmodium and Toxoplasma. ApiDB serves not only as a database in its own right, but as a single web-based point of entry that unifies access to three major existing individual organism databases (PlasmoDB.org, ToxoDB.org and CryptoDB.org), and integrates these databases with data available from additional sources. Through the ApiDB site, users may pose queries and search all available apicomplexan data and tools, or they may visit individual component organism databases.</protect>
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|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17098930 PubMed]
Online version:[http://dx.doi.org/10.1093/nar/gkl880 10.1093/nar/gkl880]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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<protect>

{| id="A4d96afe2672a5" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177516.A4d96afe2672a5&page=177516&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
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==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

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PMID:17098930

2011-04-02T05:10:58Z

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PMID:14962373

2011-04-02T05:07:24Z

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<protect>
 '''Fraunholz, MJ and Roos, DS''' (2003) PlasmoDB: exploring genomics and post-genomics data of the malaria parasite, Plasmodium falciparum.''Redox Rep.'' '''8''':317-20

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|{{TableHeadingColor}} |'''Abstract''' || <protect>The recent completion of the genome sequence of Plasmodium falciparum 3D7 provides the foundation for genome-wide analysis of the parasite. In addition to DNA and gene sequence data, postgenomic methods including microarray-based transcript profiling and high-throughput proteomics are now accessible to Plasmodium researchers. The Plasmodium Genome database (<http://PlasmoDB.org>) was developed to provide rapid and convenient access to the terabytes of genomic-scale data now being generated around the world. All data are available in a relational framework, permitting convenient downloading, browsing, and analysis. Combinatorial use of data analysis tools enables powerful data mining queries, such as combining gene and protein expression data to monitor changes through various life-cycle stages. Functional predictions can be used to explore potential targets for antimalarial drug development. This report outlines the use of PlasmoDB to examine redox-active functions in Plasmodium.</protect>
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|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14962373 PubMed]
Online version:[http://dx.doi.org/10.1179/135100003225002961 10.1179/135100003225002961]
|}
</protect>
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{{LitSignificance}}

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<protect>

{| id="G4d96af0bd051c" class=" tableEdit GO_table_reference"
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!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

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|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177515.G4d96af0bd051c&page=177515&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
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==References==
{{RefHelp}}
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PMID:14962373

2011-04-02T05:07:23Z

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PMID:17029963

2011-04-02T05:04:19Z

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<protect>
 '''Stoeckert, CJ, Fischer, S, Kissinger, JC, Heiges, M, Aurrecoechea, C, Gajria, B and Roos, DS''' (2006) PlasmoDB v5: new looks, new genomes.''Trends Parasitol.'' '''22''':543-6

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|{{TableHeadingColor}} |'''Abstract''' || <protect>Version 5.1 of PlasmoDB, a resource for malaria parasite genomic and functional genomics datasets, was released in August 2006. This new release includes additional Plasmodium genomes and a newly designed website. The new site reflects the status of PlasmoDB as a member of a linked family of Apicomplexan databases.</protect>
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|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17029963 PubMed]
Online version:[http://dx.doi.org/10.1016/j.pt.2006.09.005 10.1016/j.pt.2006.09.005]
|}
</protect>
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<protect>

{| id="F4d96ae53b1821" class=" tableEdit GO_table_reference"
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!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177514.F4d96ae53b1821&page=177514&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
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==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
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==References==
{{RefHelp}}
<references/>

PMID:17029963

2011-04-02T05:04:19Z

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PMID:19843604

2011-04-02T04:54:36Z

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<protect>
 '''Aslett, M, Aurrecoechea, C, Berriman, M, Brestelli, J, Brunk, BP, Carrington, M, Depledge, DP, Fischer, S, Gajria, B, Gao, X, Gardner, MJ, Gingle, A, Grant, G, Harb, OS, Heiges, M, Hertz-Fowler, C, Houston, R, Innamorato, F, Iodice, J, Kissinger, JC, Kraemer, E, Li, W, Logan, FJ, Miller, JA, Mitra, S, Myler, PJ, Nayak, V, Pennington, C, Phan, I, Pinney, DF, Ramasamy, G, Rogers, MB, Roos, DS, Ross, C, Sivam, D, Smith, DF, Srinivasamoorthy, G, Stoeckert, CJ, Subramanian, S, Thibodeau, R, Tivey, A, Treatman, C, Velarde, G and Wang, H''' (2010) TriTrypDB: a functional genomic resource for the Trypanosomatidae.''Nucleic Acids Res.'' '''38''':D457-62

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || <protect>TriTrypDB (http://tritrypdb.org) is an integrated database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. TriTrypDB is a collaborative project, utilizing the GUS/WDK computational infrastructure developed by the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) to integrate genome annotation and analyses from GeneDB and elsewhere with a wide variety of functional genomics datasets made available by members of the global research community, often pre-publication. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. 'User Comments' may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate.</protect>
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|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19843604 PubMed]
Online version:[http://dx.doi.org/10.1093/nar/gkp851 10.1093/nar/gkp851]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{| id="D4d96ac0c3939a" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

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|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177513.D4d96ac0c3939a&page=177513&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
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==References==
{{RefHelp}}
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PMID:19843604

2011-04-02T04:54:36Z

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PMID:16381902

2011-04-02T04:48:48Z

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<protect>
 '''Heiges, M, Wang, H, Robinson, E, Aurrecoechea, C, Gao, X, Kaluskar, N, Rhodes, P, Wang, S, He, CZ, Su, Y, Miller, J, Kraemer, E and Kissinger, JC''' (2006) CryptoDB: a Cryptosporidium bioinformatics resource update.''Nucleic Acids Res.'' '''34''':D419-22

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || <protect>The database, CryptoDB (http://CryptoDB.org), is a community bioinformatics resource for the AIDS-related apicomplexan-parasite, Cryptosporidium. CryptoDB integrates whole genome sequence and annotation with expressed sequence tag and genome survey sequence data and provides supplemental bioinformatics analyses and data-mining tools. A simple, yet comprehensive web interface is available for mining and visualizing the data. CryptoDB is allied with the databases PlasmoDB and ToxoDB via ApiDB, an NIH/NIAID-fundedBioinformatics Resource Center. Recent updates to CryptoDB include the deposition of annotated genome sequences for Cryptosporidium parvum and Cryptosporidium hominis, migration to a relational database (GUS), a new query and visualization interface and the introduction of Web services.</protect>
|-
|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16381902 PubMed]
Online version:[http://dx.doi.org/10.1093/nar/gkj078 10.1093/nar/gkj078]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{| id="L4d96aab02b8e9" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177512.L4d96aab02b8e9&page=177512&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

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

==See also==

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

PMID:16381902

2011-04-02T04:48:48Z

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PMID:16844709

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<protect>
 '''Wang, H, Su, Y, Mackey, AJ, Kraemer, ET and Kissinger, JC''' (2006) SynView: a GBrowse-compatible approach to visualizing comparative genome data.''Bioinformatics'' '''22''':2308-9

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || <protect> We present SynView, a simple and generic approach to dynamically visualize multi-species comparative genome data. It is a light-weight application based on the popular and configurable web-based GBrowse framework. It can be used with a variety of databases and provides the user with a high degree of interactivity. The tool is written in Perl and runs on top of the GBrowse framework. It is in use in the PlasmoDB (http://www.PlasmoDB.org) and the CryptoDB (http://www.CryptoDB.org) projects and can be easily integrated into other cross-species comparative genome projects. AVAILABILITY: The program and instructions are freely available at http://www.ApiDB.org/apps/SynView/ CONTACT: jkissing@uga.edu.</protect>
|-
|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16844709 PubMed]
Online version:[http://dx.doi.org/10.1093/bioinformatics/btl389 10.1093/bioinformatics/btl389]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{| id="U4d96a9cc8d3c3" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177511.U4d96a9cc8d3c3&page=177511&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

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

==See also==

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

PMID:16844709

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PMID:11839180

2011-04-02T04:41:43Z

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<protect>
 '''Roos, DS, Crawford, MJ, Donald, RG, Fraunholz, M, Harb, OS, He, CY, Kissinger, JC, Shaw, MK and Striepen, B''' (2002) Mining the Plasmodium genome database to define organellar function: what does the apicoplast do?''Philos. Trans. R. Soc. Lond., B, Biol. Sci.'' '''357''':35-46

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || <protect>Apicomplexan species constitute a diverse group of parasitic protozoa, which are responsible for a wide range of diseases in many organisms. Despite differences in the diseases they cause, these parasites share an underlying biology, from the genetic controls used to differentiate through the complex parasite life cycle, to the basic biochemical pathways employed for intracellular survival, to the distinctive cell biology necessary for host cell attachment and invasion. Different parasites lend themselves to the study of different aspects of parasite biology: Eimeria for biochemical studies, Toxoplasma for molecular genetic and cell biological investigation, etc. The Plasmodium falciparum Genome Project contributes the first large-scale genomic sequence for an apicomplexan parasite. The Plasmodium Genome Database (http://PlasmoDB.org) has been designed to permit individual investigators to ask their own questions, even prior to formal release of the reference P. falciparum genome sequence. As a case in point, PlasmoDB has been exploited to identify metabolic pathways associated with the apicomplexan plastid, or 'apicoplast' - an essential organelle derived by secondary endosymbiosis of an alga, and retention of the algal plastid.</protect>
|-
|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11839180 PubMed]
Online version:[http://dx.doi.org/10.1098/rstb.2001.1047 10.1098/rstb.2001.1047]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{| id="L4d96a906cec52" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177510.L4d96a906cec52&page=177510&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

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

==See also==

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

PMID:11839180

2011-04-02T04:41:42Z

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PMID:18003657

2011-04-02T04:37:40Z

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<protect>
 '''Gajria, B, Bahl, A, Brestelli, J, Dommer, J, Fischer, S, Gao, X, Heiges, M, Iodice, J, Kissinger, JC, Mackey, AJ, Pinney, DF, Roos, DS, Stoeckert, CJ, Wang, H and Brunk, BP''' (2008) ToxoDB: an integrated Toxoplasma gondii database resource.''Nucleic Acids Res.'' '''36''':D553-6

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || <protect>ToxoDB (http://ToxoDB.org) is a genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well as genome sequences for the GT1, VEG and RH (Chr Ia, Chr Ib) strains. Sequence information is integrated with various other genomic-scale data, including community annotation, ESTs, gene expression and proteomics data. ToxoDB has matured significantly since its initial release. Here we outline the numerous updates with respect to the data and increased functionality available on the website.</protect>
|-
|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18003657 PubMed]
Online version:[http://dx.doi.org/10.1093/nar/gkm981 10.1093/nar/gkm981]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{| id="A4d96a8142124f" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177509.A4d96a8142124f&page=177509&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

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

==See also==

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

PMID:18003657

2011-04-02T04:37:39Z

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PMID:15998914

2011-03-25T13:09:58Z

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<protect>
 '''Alm, EJ, Huang, KH, Price, MN, Koche, RP, Keller, K, Dubchak, IL and Arkin, AP''' (2005) The MicrobesOnline Web site for comparative genomics.''Genome Res.'' '''15''':1015-22

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || <protect>At present, hundreds of microbial genomes have been sequenced, and hundreds more are currently in the pipeline. The Virtual Institute for Microbial Stress and Survival has developed a publicly available suite of Web-based comparative genomic tools (http://www.microbesonline.org) designed to facilitate multispecies comparison among prokaryotes. Highlights of the MicrobesOnline Web site include operon and regulon predictions, a multispecies genome browser, a multispecies Gene Ontology browser, a comparative KEGG metabolic pathway viewer, a Bioinformatics Workbench for in-depth sequence analysis, and Gene Carts that allow users to save genes of interest for further study while they browse. In addition, we provide an interface for genome annotation, which like all of the tools reported here, is freely available to the scientific community.</protect>
|-
|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15998914 PubMed]
Online version:[http://dx.doi.org/10.1101/gr.3844805 10.1101/gr.3844805]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{| id="K4d8c94265ca53" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177466.K4d8c94265ca53&page=177466&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

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

==See also==

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

PMID:15998914

2011-03-25T13:09:57Z

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PMID:18936051

2011-03-20T14:00:47Z

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<protect>
 '''Reeves, GA, Eilbeck, K, Magrane, M, O'Donovan, C, Montecchi-Palazzi, L, Harris, MA, Orchard, S, Jimenez, RC, Prlic, A, Hubbard, TJ, Hermjakob, H and Thornton, JM''' (2008) The Protein Feature Ontology: a tool for the unification of protein feature annotations.''Bioinformatics'' '''24''':2767-72

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || <protect>The advent of sequencing and structural genomics projects has provided a dramatic boost in the number of uncharacterized protein structures and sequences. Consequently, many computational tools have been developed to help elucidate protein function. However, such services are spread throughout the world, often with standalone web pages. Integration of these methods is needed and so far this has not been possible as there was no common vocabulary available that could be used as a standard language.</protect>
|-
|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18936051 PubMed]
Online version:[http://dx.doi.org/10.1093/bioinformatics/btn528 10.1093/bioinformatics/btn528]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{| id="A4d86088ee213b" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177408.A4d86088ee213b&page=177408&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

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

==See also==

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

PMID:18936051

2011-03-20T14:00:46Z

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PMID:20138106

2011-03-20T07:47:50Z

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{{RightTOC}}
<protect>
 '''Maheshwari, A, Verma, VK and Chaudhuri, TK''' (2010) Equilibrium and kinetics of the unfolding and refolding of Escherichia coli Malate Synthase G monitored by circular dichroism and fluorescence spectroscopy.''Biochimie'' '''92''':491-8

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || <protect>The equilibrium and kinetics studies of an 82 kDa large monomeric Escherichia coli protein Malate Synthase G (MSG) was investigated by far and near-UV CD, intrinsic tryptophan fluorescence and extrinsic fluorescence spectroscopy. We find that despite of its large size, folding is reversible, in vitro. Equilibrium unfolding process of MSG exhibited three-state transition thus, indicating the presence of at least a stable equilibrium intermediate. Thermodynamic parameters suggest this intermediate resembles the unfolded state. However, the equilibrium intermediate exhibits pronounced secondary structure as measured by far-UV CD, partial tertiary structure as delineated by near-UV CD, compactness (m value) and exposed hydrophobic surface area as assessed by ANS binding, typically depicting a molten globule state. The stopped-flow kinetic data provide clear evidence for the presence of a burst phase during the refolding pathway due to the formation of an early Intermediate, within the dead time of the instrument. Refolding from 4 M to various lower concentrations until 0.4 M of GdnHCl follow biphasic kinetics at lower concentrations of GdnHCl (<0.8 M), whereas monophasic kinetics at concentrations above 1.5 M. Also, rollover in the refolding and unfolding limbs of chevron plot verifies the presence of a fast kinetic intermediate at lower concentration of GdnHCl. Based upon the above observations we hereby propose the folding pathway of a large multi-domain protein Malate Synthase G.</protect>
|-
|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20138106 PubMed]
Online version:[http://dx.doi.org/10.1016/j.biochi.2010.01.009 10.1016/j.biochi.2010.01.009]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{| id="L4d85b12598d8a" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177403.L4d85b12598d8a&page=177403&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

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

==See also==

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

PMID:20138106

2011-03-20T07:47:46Z

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PMID:19959836

2011-03-20T07:42:38Z

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{{RightTOC}}
<protect>
 '''Price, CE and Driessen, AJ''' (2010) Conserved negative charges in the transmembrane segments of subunit K of the NADH:ubiquinone oxidoreductase determine its dependence on YidC for membrane insertion.''J. Biol. Chem.'' '''285''':3575-81

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || <protect>All members of the Oxa1/Alb3/YidC family have been implicated in the biogenesis of respiratory and energy transducing proteins. In Escherichia coli, YidC functions together with and independently of the Sec system. Although the range of proteins shown to be dependent on YidC continues to increase, the exact role of YidC in insertion remains enigmatic. Here we show that YidC is essential for the insertion of subunit K of the NADH:ubiquinone oxidoreductase and that the dependence is due to the presence of two conserved glutamate residues in the transmembrane segments of subunit K. The results suggest a model in which YidC serves as a membrane chaperone for the insertion of the less hydrophobic, negatively charged transmembrane segments of NuoK.</protect>
|-
|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19959836 PubMed]
Online version:[http://dx.doi.org/10.1074/jbc.M109.051128 10.1074/jbc.M109.051128]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{| id="X4d85afee3ed03" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177402.X4d85afee3ed03&page=177402&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

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

==See also==

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

PMID:19959836

2011-03-20T07:42:37Z

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Category:GO:0009288 ! bacterial-type flagellum

2011-03-20T07:42:32Z

192.31.21.150: New GO term category page

Category:GO:0009420 ! bacterial-type flagellum filament

2011-03-20T07:17:20Z

192.31.21.150: New GO term category page

Category:GO:0005576 ! extracellular region

2011-03-20T06:56:36Z

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PMID:19933363

2011-03-17T08:27:19Z

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<protect>
 '''Bekker, M, Alexeeva, S, Laan, W, Sawers, G, Teixeira de Mattos, J and Hellingwerf, K''' (2010) The ArcBA two-component system of Escherichia coli is regulated by the redox state of both the ubiquinone and the menaquinone pool.''J. Bacteriol.'' '''192''':746-54

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || <protect>ArcBA is a two-component regulatory system of Escherichia coli involved in sensing oxygen availability and the concomitant transcriptional regulation of oxidative and fermentative catabolism. Based on in vitro data, it has been postulated that the redox state of the ubiquinone pool is the determinant for ArcB kinase activity. Here we report on the in vivo regulation of ArcB activation, as determined using a lacZ reporter specifically responsive to phosphorylated ArcA. Our results indicate that upon deletion of a ubiquinone biosynthetic enzyme, regulation of ArcB in the anaerobic-aerobic transition is not affected. In contrast, interference with menaquinone biosynthesis leads to inactivation of ArcB during anaerobic growth; this phenotype is fully rescued by addition of a menaquinone precursor. This clearly demonstrates that the menaquinones play a major role in ArcB activation. ArcB shows a complex pattern of regulation when E. coli is titrated through the entire aerobiosis range; ArcB is activated under anaerobic and subaerobic conditions and is much less active under fully aerobic and microaerobic conditions. Furthermore, there is no correlation between ArcB activation and the redox state of the ubiquinone pool, but there is a restricted correlation between the total cellular ubiquinone content and ArcB activity due to the considerable increase in the size of the ubiquinone pool with increasing degrees of aerobiosis. These results lead to the working hypothesis that the in vivo activity of ArcB in E. coli is modulated by the redox state of the menaquinone pool and that the ubiquinone/ubiquinol ratio in vivo surely is not the only determinant of ArcB activity.</protect>
|-
|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19933363 PubMed]
Online version:[http://dx.doi.org/10.1128/JB.01156-09 10.1128/JB.01156-09]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{| id="N4d81c5e7b957b" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177384.N4d81c5e7b957b&page=177384&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

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

==See also==

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

PMID:19933363

2011-03-17T08:27:19Z

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PMID:19940155

2011-03-17T08:22:18Z

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{{RightTOC}}
<protect>
 '''Tan, M, Zhu, B, Zhou, XL, He, R, Chen, X, Eriani, G and Wang, ED''' (2010) tRNA-dependent pre-transfer editing by prokaryotic leucyl-tRNA synthetase.''J. Biol. Chem.'' '''285''':3235-44

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || <protect>To prevent genetic code ambiguity due to misincorporation of amino acids into proteins, aminoacyl-tRNA synthetases have evolved editing activities to eliminate intermediate or final non-cognate products. In this work we studied the different editing pathways of class Ia leucyl-tRNA synthetase (LeuRS). Different mutations and experimental conditions were used to decipher the editing mechanism, including the recently developed compound AN2690 that targets the post-transfer editing site of LeuRS. The study emphasizes the crucial importance of tRNA for the pre- and post-transfer editing catalysis. Both reactions have comparable efficiencies in prokaryotic Aquifex aeolicus and Escherichia coli LeuRSs, although the E. coli enzyme favors post-transfer editing, whereas the A. aeolicus enzyme favors pre-transfer editing. Our results also indicate that the entry of the CCA-acceptor end of tRNA in the editing domain is strictly required for tRNA-dependent pre-transfer editing. Surprisingly, this editing reaction was resistant to AN2690, which inactivates the enzyme by forming a covalent adduct with tRNA(Leu) in the post-transfer editing site. Taken together, these data suggest that the binding of tRNA in the post-transfer editing conformation confers to the enzyme the capacity for pre-transfer editing catalysis, regardless of its capacity to catalyze post-transfer editing.</protect>
|-
|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19940155 PubMed]
Online version:[http://dx.doi.org/10.1074/jbc.M109.060616 10.1074/jbc.M109.060616]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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

{| id="T4d81c4ba219ac" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177383.T4d81c4ba219ac&page=177383&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

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

==See also==

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

PMID:19940155

2011-03-17T08:22:18Z

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PMID:20043916

2011-03-17T08:17:16Z

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<protect>
 '''Liu, Z, Madej, MG and Kaback, HR''' (2010) Helix dynamics in LacY: helices II and IV.''J. Mol. Biol.'' '''396''':617-26

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|{{TableHeadingColor}} |'''Abstract''' || <protect>Biochemical and biophysical studies based upon crystal structures of both a mutant and wild-type lactose permease from Escherichia coli (LacY) in an inward-facing conformation have led to a model for the symport mechanism in which both sugar and H+ binding sites are alternatively accessible to both sides of the membrane. Previous findings indicate that the face of helix II with Asp68 is important for the conformational changes that occur during turnover. As shown here, replacement of Asp68 at the cytoplasmic end of helix II, particularly with Glu, abolishes active transport but the mutants retain the ability to bind galactopyranoside. In the x-ray structure, Asp68 and Lys131 (helix IV) lie within approximately 4.2 A of each other. Although a double mutant with Cys replacements at both position 68 and position 131 cross-links efficiently, single replacements for Lys131 exhibit very significant transport activity. Site-directed alkylation studies show that sugar binding by the Asp68 mutants causes closure of the cytoplasmic cavity, similar to wild-type LacY; however, strikingly, the probability of opening the periplasmic pathway upon sugar binding is markedly reduced. Taken together with results from previous mutagenesis and cross-linking studies, these findings lead to a model in which replacement of Asp68 blocks a conformational transition involving helices II and IV that is important for opening the periplasmic cavity. Evidence suggesting that movements of helices II and IV are coupled functionally with movements in the pseudo-symmetrically paired helices VIII and X is also presented.</protect>
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|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20043916 PubMed]
Online version:[http://dx.doi.org/10.1016/j.jmb.2009.12.044 10.1016/j.jmb.2009.12.044]
|}
</protect>
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{| id="L4d81c38c73b6b" class=" tableEdit GO_table_reference"
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!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

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|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177382.L4d81c38c73b6b&page=177382&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
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PMID:20043916

2011-03-17T08:17:16Z

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PMID:19916164

2011-03-17T08:07:14Z

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<protect>
 '''Koutsioulis, D, Lyskowski, A, Mäki, S, Guthrie, E, Feller, G, Bouriotis, V and Heikinheimo, P''' (2010) Coordination sphere of the third metal site is essential to the activity and metal selectivity of alkaline phosphatases.''Protein Sci.'' '''19''':75-84

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|{{TableHeadingColor}} |'''Abstract''' || <protect>Alkaline phosphatases (APs) are commercially applied enzymes that catalyze the hydrolysis of phosphate monoesters by a reaction involving three active site metal ions. We have previously identified H135 as the key residue for controlling activity of the psychrophilic TAB5 AP (TAP). In this article, we describe three X-ray crystallographic structures on TAP variants H135E and H135D in complex with a variety of metal ions. The structural analysis is supported by thermodynamic and kinetic data. The AP catalysis essentially requires octahedral coordination in the M3 site, but stability is adjusted with the conformational freedom of the metal ion. Comparison with the mesophilic Escherichia coli, AP shows differences in the charge transfer network in providing the chemically optimal metal combination for catalysis. Our results provide explanation why the TAB5 and E. coli APs respond in an opposite way to mutagenesis in their active sites. They provide a lesson on chemical fine tuning and the importance of the second coordination sphere in defining metal specificity in enzymes. Understanding the framework of AP catalysis is essential in the efforts to design even more powerful tools for modern biotechnology.</protect>
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|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19916164 PubMed]
Online version:[http://dx.doi.org/10.1002/pro.284 10.1002/pro.284]
|}
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<protect>

{| id="D4d81c131e6b94" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177381.D4d81c131e6b94&page=177381&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
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PMID:19916164

2011-03-17T08:07:13Z

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PMID:19932117

2011-03-17T07:47:09Z

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<protect>
 '''Dhakshnamoorthy, B, Raychaudhury, S, Blachowicz, L and Roux, B''' (2010) Cation-selective pathway of OmpF porin revealed by anomalous X-ray diffraction.''J. Mol. Biol.'' '''396''':293-300

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|{{TableHeadingColor}} |'''Abstract''' || <protect>The OmpF porin from the Escherichia coli outer membrane folds into a trimer of beta-barrels, each forming a wide aqueous pore allowing the passage of ions and small solutes. A long loop (L3) carrying multiple acidic residues folds into the beta-barrel pore to form a narrow "constriction zone". A strong and highly conserved charge asymmetry is observed at the constriction zone, with multiple basic residues attached to the wall of the beta-barrel (Lys16, Arg42, Arg82 and Arg132) on one side, and multiple acidic residues of L3 (Asp107, Asp113, Glu117, Asp121, Asp126, Asp127) on the other side. Several computational studies have suggested that a strong transverse electric field could exist at the constriction zone as a result of such charge asymmetry, giving rise to separate permeation pathways for cations and anions. To examine this question, OmpF was expressed, purified and crystallized in the P6(3) space group and two different data sets were obtained at 2.6 A and 3.0 A resolution with K(+) and Rb(+), respectively. The Rb(+)-soaked crystals were collected at the rubidium anomalous wavelength of 0.8149 A and cation positions were determined. A PEG molecule was observed in the pore region for both the K(+) and Rb(+)-soaked crystals, where it interacts with loop L3. The results reveal the separate pathways of anions and cations across the constriction zone of the OmpF pore.</protect>
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|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19932117 PubMed]
Online version:[http://dx.doi.org/10.1016/j.jmb.2009.11.042 10.1016/j.jmb.2009.11.042]
|}
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{| id="G4d81bc7d4c608" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177380.G4d81bc7d4c608&page=177380&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
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PMID:19932117

2011-03-17T07:47:09Z

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PMID:20088519

2011-03-17T07:42:07Z

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<protect>
 '''Wang, SC, Li, Y, Robinson, CV and Zamble, DB''' (2010) Potassium is critical for the Ni(II)-responsive DNA-binding activity of Escherichia coli NikR.''J. Am. Chem. Soc.'' '''132''':1506-7

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|{{TableHeadingColor}} |'''Abstract''' || <protect>The Escherichia coli NikR transcription factor is a Ni(II)-dependent repressor that regulates the production of a nickel ion transporter. The X-ray crystal structure of the Ni(II)-NikR-DNA bound complex revealed a K(+)-binding site positioned at the interface of the metal- and DNA-binding domains, but the significance of the potassium was unclear. Mutation of one of the K(+) ligands impairs the affinity and specificity of DNA binding in the presence of either stoichiometric or excess Ni(II). Removal of K(+) abrogates Ni(II)-responsive DNA binding completely while the addition of K(+) restores this activity. Furthermore, the observed K(+) dependence can be relieved by replacing the K(+) ligand Asp34 with an arginine. These mutagenesis and cation exchange experiments reveal that K(+) is a critical structural component for the activation of Ni(II)-responsive DNA binding by NikR.</protect>
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|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20088519 PubMed]
Online version:[http://dx.doi.org/10.1021/ja909136h 10.1021/ja909136h]
|}
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{| id="L4d81bb4f34b82" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.177378.L4d81bb4f34b82&page=177378&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
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PMID:20088519

2011-03-17T07:42:06Z

192.31.21.150: New PMID: Page!