PckA - Revision history

134.76.70.252 at 09:57, 17 April 2014

2014-04-17T09:57:06Z

134.76.38.147 at 14:34, 2 April 2014

2014-04-02T14:34:43Z

134.76.70.252 at 11:31, 7 January 2014

2014-01-07T11:31:00Z

134.76.70.252 at 09:11, 12 November 2013

2013-11-12T09:11:28Z

134.76.70.252 at 14:22, 16 May 2013

2013-05-16T14:22:44Z

134.76.70.252 at 11:04, 14 May 2013

2013-05-14T11:04:57Z

134.76.70.252 at 13:40, 13 May 2013

2013-05-13T13:40:27Z

Jstuelk: /* References */

2012-11-10T11:03:48Z

‎References

Fmeyer: /* Biological materials */

2012-11-02T08:32:53Z

‎Biological materials

Jstuelk: /* Biological materials */

2012-10-30T16:07:55Z

‎Biological materials

← Older revision		Revision as of 09:57, 17 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' phosphoenolpyruvate carboxykinase <br/><br/>~~	+	{{#bank: PckA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''pckA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ppc''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| phosphoenolpyruvate carboxykinase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| synthesis of phosphoenolpyruvate~~
−	\|-
−	\|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=BSU30560 pckA]
−	\|-
−	\|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=PckA PckA]
−	\|-
−	\|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=pckA pckA]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 58,1 kDa, 5.12~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1581 bp, 527 amino acids~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[metK]]'', ''[[ytmB]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU30560 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU30560 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU30560 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:pckA_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=pckA_3129530_3131113_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:pckA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU30560]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−
−
−	~~<br/><br/><br/><br/><br/><br/>~~
−
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[carbon core metabolism]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CcpN regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU30560
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU30560&redirect=T BSU30560]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pckA.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11841]
−
−	~~=== Additional information===~~
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO<sub>2</sub> (according to Swiss-Prot) ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO(2)
−
−	* '''Protein family:''' phosphoenolpyruvate carboxykinase [ATP] family (according to Swiss-Prot) phosphoenolpyruvate carboxykinase [ATP] family
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−	** Nucleotide binding Domain (233–240)
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[Mdh]]-[[PckA]] (this interaction occurs under gluconeogenic, but not under glycolytic conditions) {{PubMed\|20933603}}
−
−	* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot), cytoplasm
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU30560&redirect=T BSU30560]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2PXZ 2PXZ] (''E.coli'')
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P54418 P54418]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU30560]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.1.49 4.1.1.49]
−
−	~~=== Additional information===~~
−
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' ''[[pckA]]'' {{PubMed\|9387221}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pckA_3129530_3131113_1 pckA] {{PubMed\|22383849}}
−
−	* '''Sigma factor:''' [[SigA]] {{PubMed\|15720552}}
−
−	* '''Regulation:'''
−	** repressed by glucose (35-fold) [[CcpN]] {{PubMed\|15720552,12850135}}
−
−	* '''Regulatory mechanism:'''
−	** [[CcpN]]: transcription repression {{PubMed\|15720552}}
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** 1A1005 ( ''pckA''::''spec''), {{PubMed\| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A1005&Search=1A1005 BGSC]
−	** 1A996 ( ''pckA''::''spec''), {{PubMed\| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A996&Search=1A996 BGSC]
−	** GP1147 (''pckA''::''neo''), available in [[Jörg Stülke]]'s lab
−
−	* '''Expression vector:'''
−	** pGP1753 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Jörg Stülke]]'s lab)
−	** pGP1762 (for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Jörg Stülke]]'s lab)
−	** pGP1763 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Jörg Stülke]]'s lab)
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:''' GP1430 (spc, based on [[pGP1870]]), available in the [[Stülke]] lab
−
−	* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
−
−	* '''Antibody:'''
−
−	* '''FLAG-tag construct:'''
−	** GP1129 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab
−
−	~~=Labs working on this gene/protein=~~
−
−	~~[[Stephane Aymerich \|Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>12850135 15720552 18586936, 9387221 20933603 22190493 23136871</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 63: / Line 63: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pckA.html]
@@ Line 101: / Line 102: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2PXZ 2PXZ] (''E.coli'')

@@ 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=PckA PckA]
 |-
-|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]'''
+|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=pckA pckA]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 58,1 kDa, 5.12

@@ 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=BSU30560 pckA]
 |-
-|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/PckA PckA]
+|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=PckA PckA]
 |-
 |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]'''

@@ Line 33: / Line 33: @@
   <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=pckA_3129530_3131113_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:pckA_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pckA_3129530_3131113_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:pckA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU30560]]
 |-
 |}

@@ Line 26: / Line 26: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[metK]]'', ''[[ytmB]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU30560 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU30560 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU30560 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU30560 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU30560 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU30560 DNA_with_flanks]
 |-
 |-

@@ Line 159: / Line 159: @@
 =References=
-<pubmed>12850135 15720552 18586936, 9387221 20933603 22190493 </pubmed>
+<pubmed>12850135 15720552 18586936, 9387221 20933603 22190493 23136871</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 142: / Line 142: @@
 * '''lacZ fusion:'''
-* '''GFP fusion:'''
+* '''GFP fusion:''' GP1430 (spc, based on [[pGP1870]]), available in the [[Stülke]] lab
 * '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab

@@ Line 136: / Line 136: @@
 * '''Expression vector:'''
-** pGP1753 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
+** pGP1753 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Jörg Stülke]]'s lab)
-** pGP1762 (for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Stülke]] lab)
+** pGP1762 (for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Jörg Stülke]]'s lab)
-** pGP1763 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Stülke]] lab)
+** pGP1763 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Jörg Stülke]]'s lab)
 * '''lacZ fusion:'''
@@ Line 144: / Line 144: @@
 * '''GFP fusion:'''
-* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
 * '''Antibody:'''
-* '''FLAG-tag construct:''' GP1129 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab
+* '''FLAG-tag construct:'''
 =Labs working on this gene/protein=