PycA - Revision history

Jstuelk at 11:04, 30 July 2015

2015-07-30T11:04:52Z

Jstuelk at 09:35, 30 July 2015

2015-07-30T09:35:38Z

Fabian Commichau: /* Biological materials */

2014-12-08T13:40:49Z

‎Biological materials

Jstuelk at 17:20, 16 May 2014

2014-05-16T17:20:12Z

134.76.70.252 at 14:13, 17 April 2014

2014-04-17T14:13:07Z

134.76.70.252 at 09:44, 17 April 2014

2014-04-17T09:44:23Z

134.76.38.147 at 13:37, 2 April 2014

2014-04-02T13:37:39Z

134.76.70.252 at 10:42, 7 January 2014

2014-01-07T10:42:03Z

Jstuelk at 09:00, 25 November 2013

2013-11-25T09:00:48Z

Aklewing: /* Biological materials */

2013-08-13T12:10:35Z

‎Biological materials

← Older revision		Revision as of 11:04, 30 July 2015
Line 1:		Line 1:
−	* '''Description:~~''' pyruvate carboxylase <br/><br/>~~	+	{{#bank: PycA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''pycA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ylaP ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| pyruvate carboxylase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| replenishment of the oxaloacetate pool~~
−	\|-
−	\|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=BSU14860 pycA]
−	\|-
−	\|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=pycA pycA]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 127 kDa, 5.407~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 3444 bp, 1148 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ftsW]]'', ''[[ctaA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU14860 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU14860 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU14860 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:pycA_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=pycA_1554185_1557631_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:pycA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14860]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[carbon core metabolism]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[stringent response]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU14860
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU14860&redirect=T BSU14860]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ftsW-pycA.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12660]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:''' biotin
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−	** membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
−	** cytoplasm (homogeneously distributed throughout the cell) {{PubMed\|24825009}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU14860&redirect=T BSU14860]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3BG5 3BG5] (''S. aureus'')
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/Q9KWU4 Q9KWU4]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14860]
−
−	* '''E.C. number:''' 6.4.1.1
−
−	~~=== Additional information===~~
−	~~PycA binds to StrepTactin, and may be co-purified when purifying Strep-tagged proteins by [[SPINE]].~~
−
−	~~PycA is subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[pycA]]'' {{PubMed\|20081037}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pycA_1554185_1557631_1 pycA] {{PubMed\|22383849}}
−
−	* '''Sigma factor:''' [[SigA]] {{PubMed\|20081037}}
−
−	* '''Regulation:'''
−	** subject to positive stringent control upon lysine starvation {{PubMed\|20081037}}
−
−	* '''Regulatory mechanism:'''
−	** stringent response: due to presence of adenines at +1 and +2 positions of the transcript {{PubMed\|20081037}}
−
−	* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 2222 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 6831 {{PubMed\|24696501}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 1602 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 907 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 2037 {{PubMed\|21395229}}
−
−	~~=Biological materials =~~
−	* '''Mutant:'''
−	** GP793 (cat), available in [[Jörg Stülke]]'s lab
−
−	* '''Expression vector:'''
−	** pGP1289 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>18613815 12769720 10229653 9597748 7780827 </pubmed>~~
−	~~==Original publications==~~
−	~~<pubmed>18763711, 20081037 24825009 25755103</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 151: / Line 151: @@
 <pubmed>18613815 12769720 10229653 9597748 7780827 </pubmed>
 ==Original publications==
-<pubmed>18763711, 20081037 24825009</pubmed>
+<pubmed>18763711, 20081037 24825009 25755103</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 129: / Line 129: @@
 =Biological materials =
-* '''Mutant:''' GP793 (cat), available in [[Jörg Stülke]]'s lab
+* '''Mutant:'''
 * '''Expression vector:'''

@@ Line 62: / Line 62: @@
 === Additional information===
 =The protein=
@@ Line 90: / Line 87: @@
 * '''[[SubtInteract|Interactions]]:'''
-* '''[[Localization]]:''' membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+* '''[[Localization]]:'''
 === Database entries ===
@@ Line 151: / Line 150: @@
 <pubmed>18613815 12769720 10229653 9597748 7780827 </pubmed>
 ==Original publications==
-<pubmed>18763711, 20081037</pubmed>
+<pubmed>18763711, 20081037 24825009</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 125: / Line 125: @@
 ** number of protein molecules per cell (minimal medium with glucose and ammonium): 2222 {{PubMed|24696501}}
 ** number of protein molecules per cell (complex medium with amino acids, without glucose): 6831 {{PubMed|24696501}}
 =Biological materials =
 * '''Mutant:''' GP793 (cat), available in [[Jörg Stülke]]'s lab

← Older revision		Revision as of 09:44, 17 April 2014
Line 123:		Line 123:

	* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]		* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 2222 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 6831 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 55: / Line 55: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ftsW-pycA.html]
@@ Line 92: / Line 93: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3BG5 3BG5] (''S. aureus'')

@@ 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=BSU14860 pycA]
 |-
-|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/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/biotin/index.html Biotin]'''
+|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=pycA pycA]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 127 kDa, 5.407

@@ Line 83: / Line 83: @@
 * '''Modification:'''
-* '''Cofactor(s):''' biotin
+* '''[[Cofactors]]:''' biotin
 * '''Effectors of protein activity:'''