CdaR - Revision history

Jstuelk: /* Categories containing this gene/protein */

2015-08-05T13:06:02Z

‎Categories containing this gene/protein

Jstuelk: /* Extended information on the protein */

2015-08-05T13:05:22Z

‎Extended information on the protein

Jstuelk: /* Original publications */

2015-08-05T12:59:43Z

‎Original publications

Jstuelk: /* References */

2015-04-17T15:52:15Z

‎References

134.76.70.252 at 11:25, 17 April 2014

2014-04-17T11:25:03Z

134.76.38.147 at 12:52, 2 April 2014

2014-04-02T12:52:01Z

Jstuelk: /* Extended information on the protein */

2014-01-16T09:58:23Z

‎Extended information on the protein

134.76.70.252 at 10:02, 7 January 2014

2014-01-07T10:02:59Z

134.76.70.252 at 14:12, 18 November 2013

2013-11-18T14:12:54Z

Jstuelk: /* References */

2013-08-13T18:05:17Z

‎References

← Older revision		Revision as of 13:06, 5 August 2015
Line 1:		Line 1:
−	* '''Description:~~''' effector protein controlling [[CdaA]] diadenylate cyclase activity <br/><br/>~~	+	{{#bank: CdaR}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''cdaR''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ybbR''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| effector protein controlling [[CdaA]] diadenylate cyclase activity~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| regulation of c-di-AMP synthesis~~
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01760 cdaR]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=CdaR CdaR]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Metabolic function and regulation of this protein in [[SubtiPathways\|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=cdaR cdaR]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 52 kDa, 4.719~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1449 bp, 483 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[cdaA]]'', ''[[glmM]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU01760 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU01760 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU01760 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ybbR_context.gif]]~~
−	~~<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>~~
−	\|-
−	\|colspan="2" \|'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybbR_197027_198478_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ybbR_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01760]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[metabolism of signalling nucleotides]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU01760
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU01760&redirect=T BSU01760]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12703]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** stimulates [[CdaA]] activity upon protein-protein interaction {{PubMed\|23192352}}
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[CdaA]]-[[CdaR]], to stimulate [[CdaA]] activity {{PubMed\|26240071,23192352}}
−
−	* '''[[Localization]]:'''
−	** cell membrane, oriented towards the outside {{PubMed\|26240071}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU01760&redirect=T BSU01760]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O34659 O34659]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01760]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[cdaA]]-[[cdaR]]-[[glmM]]-[[glmS]]'' {{PubMed\|23192352}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybbR_197027_198478_1 cdaR] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|22211522}}
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:''' the ''[[cdaA]]-[[cdaR]]'' part of the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 60 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 138 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** GP999 (''[[cdaR]]''::''cat''), available in [[Jörg Stülke]]'s lab
−	** GP985 (''[[cdaA]]''-''[[cdaR]]''::''cat''), available in [[Jörg Stülke]]'s lab
−
−	* '''Expression vector:'''
−	** IPTG inducible expression of Strep-''cdaR'' in ''E. coli'': pGP2565 (in [[pGP172]]), available in [[Jörg Stülke]]'s lab
−	** IPTG inducible expression of His-''cdaR'' in ''E. coli'': pGP2557 (in [http://biochem.web.utah.edu/hill/links/pET19b.pdf pET19b]), available in [[Jörg Stülke]]'s lab
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab. Respective plasmids: pGP1989 and pGP1992.
−
−	* '''Strep-tag construct:'''
−	** GP1330 (aphA3, based on [[pGP1460]]), available in [[Jörg Stülke]]'s lab
−	** GP1380 ''lacA::cdaR-Strep aphA3 glmM-3xFLAG ermC'' (based on [[pGP1460]] and [[pGP1087]]), available in [[Jörg Stülke]]'s lab
−
−	* '''Antibody:''' available in [[Jörg Stülke]]'s lab
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed> 25869574</pubmed>~~
−	~~==Original publications==~~
−	~~<pubmed>12884008, 16236721,26240071 23192352 22211522,21154411</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 91: / Line 91: @@
 * '''[[SubtInteract|Interactions]]:'''
-** [[CdaA]]-[[CdaR]], to stimulate [[CdaA]] activity {{PubMed|23192352}}
+** [[CdaA]]-[[CdaR]], to stimulate [[CdaA]] activity {{PubMed|26240071,23192352}}
 * '''[[Localization]]:'''
 === Database entries ===

@@ Line 154: / Line 154: @@
 <pubmed> 25869574</pubmed>
 ==Original publications==
-<pubmed>12884008, 16236721, 23192352 22211522,21154411</pubmed>
+<pubmed>12884008, 16236721,26240071  23192352 22211522,21154411</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 151: / Line 151: @@
 =References=
 <pubmed>12884008, 16236721, 23192352 22211522,21154411</pubmed>
 [[Category:Protein-coding genes]]

← Older revision		Revision as of 11:25, 17 April 2014
Line 121:		Line 121:

	* '''Additional information:''' the ''[[cdaA]]-[[cdaR]]'' part of the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]		* '''Additional information:''' the ''[[cdaA]]-[[cdaR]]'' part of the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 60 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 138 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 56: / Line 56: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 95: / Line 96: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 81: / Line 81: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''

@@ Line 18: / Line 18: @@
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=CdaR CdaR]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=cdaR cdaR]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 4.719

@@ Line 16: / Line 16: @@
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01760 cdaR]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/CdaR CdaR]
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=CdaR CdaR]
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''