OdhA - Revision history

Fabian Commichau: /* Biological materials */

2014-12-08T13:45:29Z

‎Biological materials

134.76.70.252 at 14:11, 17 April 2014

2014-04-17T14:11:01Z

134.76.70.252 at 09:55, 17 April 2014

2014-04-17T09:55:55Z

134.76.38.147 at 13:55, 2 April 2014

2014-04-02T13:55:13Z

134.76.70.252 at 10:57, 7 January 2014

2014-01-07T10:57:34Z

Jstuelk at 09:54, 17 December 2013

2013-12-17T09:54:48Z

134.76.70.252 at 08:35, 12 November 2013

2013-11-12T08:35:59Z

Jstuelk: /* Biological materials */

2013-08-13T14:09:33Z

‎Biological materials

Aklewing: /* Biological materials */

2013-08-13T12:11:58Z

‎Biological materials

Jstuelk at 14:20, 12 August 2013

2013-08-12T14:20:55Z

← Older revision		Revision as of 13:45, 8 December 2014
Line 1:		Line 1:
−	* '''Description:~~''' 2-oxoglutarate dehydrogenase (E1 subunit) <br/><br/>~~	+	{{#bank: OdhA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''odhA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''citK ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| 2-oxoglutarate dehydrogenase (E1 subunit)~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| TCA cycle~~
−	\|-
−	\|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=BSU19370 odhA]
−	\|-
−	\|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=OdhA OdhA]
−	\|-
−	\|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=odhA odhA]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 105 kDa, 5.871~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 2823 bp, 941 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[odhB]], [[yojO]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU19370 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU19370 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU19370 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:odhA_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=odhA_2108774_2111608_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:odhA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU19370]]
−	\|-
−	\|}
−
−	~~__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\|[[phosphoproteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CcpA regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU19370
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU19370&redirect=T BSU19370]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/odhAB.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10272]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' 2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO<sub>2</sub> (according to Swiss-Prot)
−
−	* '''Protein family:''' 2-oxoacid dehydrogenase family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−	** phosphorylated on Arg-66 and Arg-621 {{PubMed\|22517742}}
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[OdhA]]-[[OdhB]]-[[PdhD]] {{PubMed\|20933603}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU19370&redirect=T BSU19370]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2jgd 2JGD] (from ''Escherichia coli'', 38% identity, 55% similarity) {{PubMed\|17367808}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P23129 P23129]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU19370]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.4.2 1.2.4.2]
−
−	~~=== Additional information===~~
−	* extensive information on the structure and enzymatic properties of 2-oxoglutarate dehydrogenase can be found at [http://www.proteopedia.org/wiki/index.php/2-Oxoglutarate_Dehydrogenase Proteopedia]
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[odhA]]''-''[[odhB]]'' {{PubMed\|11976317}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=odhA_2108774_2111608_-1 odhA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|1508153}}
−
−	* '''Regulation:'''
−	** repressed by glucose (2.4-fold) ([[CcpA]]) {{PubMed\|12850135}}
−
−	* '''Regulatory mechanism:'''
−	** [[CcpA]]: transcription repression {{PubMed\|12850135}}
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 2760 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 30660 {{PubMed\|24696501}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 2474 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 2111 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 3918 {{PubMed\|21395229}}
−
−	~~=Biological materials =~~
−	* '''Mutant:'''
−	** GP671 (spc), GP684 (cat), GP1274 (cat) available in [[Jörg Stülke]]'s lab
−	** GP1276 (''[[odhA]]-[[odhB]]''::''cat''), available in [[Jörg Stülke]]'s lab
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed> 10672230</pubmed>~~
−	~~==Original publications==~~
−	~~<pubmed>2500417,20933603,1508153, 11976317 12850135 22517742 22900538 24263382 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 126: / Line 126: @@
 ** number of protein molecules per cell (minimal medium with glucose and ammonium): 2760 {{PubMed|24696501}}
 ** number of protein molecules per cell (complex medium with amino acids, without glucose): 30660 {{PubMed|24696501}}
 =Biological materials =
 * '''Mutant:'''
 ** GP671 (spc), GP684 (cat), GP1274 (cat) available in [[Jörg Stülke]]'s lab

← Older revision		Revision as of 09:55, 17 April 2014
Line 124:		Line 124:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 2760 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 30660 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 59: / Line 59: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/odhAB.html]
@@ Line 95: / Line 96: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2jgd 2JGD] (from ''Escherichia coli'', 38% identity, 55% similarity)	{{PubMed|17367808}}

@@ 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=OdhA OdhA]
 |-
-|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=odhA odhA]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 105 kDa, 5.871

@@ Line 80: / Line 80: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
 ** phosphorylated on Arg-66 and Arg-621 {{PubMed|22517742}}
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 113: / Line 113: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=odhA_2108774_2111608_-1 odhA] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] {{PubMed|1508153}}
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|1508153}}
 * '''Regulation:'''
@@ Line 147: / Line 147: @@
 <pubmed> 10672230</pubmed>
 ==Original publications==
-<pubmed>2500417,20933603,1508153, 11976317 12850135 22517742 22900538 </pubmed>
+<pubmed>2500417,20933603,1508153, 11976317 12850135 22517742 22900538 24263382 </pubmed>
 [[Category:Protein-coding genes]]

@@ 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=BSU19370 odhA]
 |-
-|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/OdhA OdhA]
+|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=OdhA OdhA]
 |-
 |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 125: / Line 125: @@
 =Biological materials =
-* '''Mutant:''' GP671 (spc), GP684 (cat), GP1274 (cat) available in [[Jörg Stülke]]'s lab
+* '''Mutant:'''
-** GP1276 (''odhAB''::''cat''), available in [[Jörg Stülke]]'s lab
+** GP671 (spc), GP684 (cat), GP1274 (cat) available in [[Jörg Stülke]]'s lab
 * '''Expression vector:'''

@@ Line 41: / Line 41: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 120: / Line 120: @@
 * '''Regulatory mechanism:'''
 ** [[CcpA]]: transcription repression {{PubMed|12850135}}
 * '''Additional information:'''
@@ Line 126: / Line 125: @@
 =Biological materials =
-* '''Mutant:''' GP671 (spc), GP684 (cat), available in [[Stülke]] lab
+* '''Mutant:''' GP671 (spc), GP684 (cat), available in [[Jörg Stülke]]'s lab
 * '''Expression vector:'''
@@ Line 134: / Line 133: @@
 * '''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:'''