PdhC - Revision history

Jstuelk: /* Reviews */

2014-05-28T13:51:41Z

‎Reviews

Jstuelk at 17:21, 16 May 2014

2014-05-16T17:21:16Z

134.76.70.252 at 14:11, 17 April 2014

2014-04-17T14:11:31Z

134.76.70.252 at 09:43, 17 April 2014

2014-04-17T09:43:41Z

134.76.38.147 at 13:36, 2 April 2014

2014-04-02T13:36:48Z

Jstuelk at 13:21, 5 March 2014

2014-03-05T13:21:44Z

134.76.70.252 at 10:41, 7 January 2014

2014-01-07T10:41:20Z

134.76.70.252 at 16:10, 11 November 2013

2013-11-11T16:10:22Z

Jstuelk: /* Extended information on the protein */

2013-07-28T10:50:47Z

‎Extended information on the protein

Jstuelk at 19:14, 8 June 2013

2013-06-08T19:14:59Z

← Older revision		Revision as of 13:51, 28 May 2014
Line 1:		Line 1:
−	* '''Description:~~''' pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) <br/><br/>~~	+	{{#bank: PdhC}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''pdhC''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| pyruvate dehydrogenase <br/>(dihydrolipoamide acetyltransferase E2 subunit)~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| links glycolysis and 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=BSU14600 pdhC]
−	\|-
−	\|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=PdhC PdhC]
−	\|-
−	\|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=pdhC pdhC]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 47 kDa, 4.855~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1326 bp, 442 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[pdhB]]'', ''[[pdhD]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU14600 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU14600 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU14600 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:pdhC_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=pdhC_1530537_1531865_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:pdhC_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14600]]
−	\|-
−	\|}
−
−	~~__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]]}},~~
−	~~[[most abundant proteins]]~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[stringent response]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU14600
−
−	~~===Phenotypes of a mutant ===~~
−
−	* defects in sporulation and unable to grow on glucose as single carbon source [http://www.ncbi.nlm.nih.gov/pubmed/11976308 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU14600&redirect=T BSU14600]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pdhABCD.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10209]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-acetyldihydrolipoyl)lysine (according to Swiss-Prot)
−
−	* '''Protein family:''' lipoyl-binding domain (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):''' [[AcoC]], [[BkdB]], [[OdhB]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:''' phosphorylated (Ser/Thr/Tyr) [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
−
−	* '''[[Cofactors]]:'''
−	** lipoic acid
−
−	* '''Effectors of protein activity:'''
−	** Inhibited by thiamine 2-thiothiazolone diphosphate and NADH [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]
−	** Low sensibility to NADPH
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[PdhA]]-[[PdhB]]-[[PdhC]]-[[PdhD]]
−
−	* '''[[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=BSU14600&redirect=T BSU14600]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1W88 1W88] (E1 in complex with subunit binding domain of E2, ''Geobacillus stearothermophilus''), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2PDE 2PDE] (peripheral subunit binding domain, ''Geobacillus stearothermophilus''), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1LAC 1LAC] (lipoyl domain, ''Geobacillus stearothermophilus''), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1B5S 1B5S] (catalytic domain (residues 184-425) , ''Geobacillus stearothermophilus'')
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P21883 P21883]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14600]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.1.12 2.3.1.12] 2
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:'''
−	** ''[[pdhA]]-[[pdhB]]-[[pdhC]]-[[pdhD]]'' {{PubMed\|11976308}}
−	** ''[[pdhC]]-[[pdhD]]'' {{PubMed\|11976308}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pdhC_1530537_1531865_1 pdhC] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−	** ''[[pdhA]]'': [[SigA]] {{PubMed\|20081037}}
−	** ''[[pdhC]]'': [[SigA]] {{PubMed\|11976308}}
−
−	* '''Regulation:'''
−	** ''[[pdhA]]'': expression activated by glucose (1.9-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
−	** subject to negative stringent control upon amino acid limitation {{PubMed\|20081037}}
−
−	* '''Regulatory mechanism:'''
−	** stringent response: due to presence of guanine at +1 position of the transcript {{PubMed\|20081037}}
−	** belongs to the 100 [[most abundant proteins]] {{PubMed\|15378759}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 11281 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 33899 {{PubMed\|24696501}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 10012 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 6860 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 6154 {{PubMed\|21395229}}
−
−	~~=Biological materials =~~
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~[[Arthur Aronson]], Purdue University, West Lafayette, USA [http://wwwdev.gradschool.purdue.edu/PULSe/faculty.cfm?fid=5&range=0 homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed> 19476487 9655937 2227213 6805383 1794583 </pubmed>~~
−	~~==Original publications==~~
−	~~<pubmed>9352926,24825009, 9352926,17726680 ,12850135 18763711 6414463 11976308 20081037 22862776 15378759</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 96: / Line 96: @@
 ** [[PdhA]]-[[PdhB]]-[[PdhC]]-[[PdhD]]
-* '''[[Localization]]:''' membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+* '''[[Localization]]:'''
 === Database entries ===
@@ Line 158: / Line 160: @@
 <pubmed> 19476487 9655937 2227213 6805383 1794583 </pubmed>
 ==Original publications==
-<pubmed>9352926,, 9352926,17726680 ,12850135 18763711 6414463 11976308 20081037 22862776 15378759</pubmed>
+<pubmed>9352926,24825009, 9352926,17726680 ,12850135 18763711 6414463 11976308 20081037 22862776 15378759</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 131: / Line 131: @@
 ** number of protein molecules per cell (minimal medium with glucose and ammonium): 11281 {{PubMed|24696501}}
 ** number of protein molecules per cell (complex medium with amino acids, without glucose): 33899 {{PubMed|24696501}}
 =Biological materials =
 * '''Mutant:'''

@@ Line 129: / Line 129: @@
 ** stringent response: due to presence of guanine at +1 position of the transcript {{PubMed|20081037}}
 ** belongs to the 100 [[most abundant proteins]] {{PubMed|15378759}}
 =Biological materials =

@@ Line 60: / Line 60: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pdhABCD.html]
@@ Line 98: / Line 99: @@
 === Database entries ===
 * '''Structure:'''	[http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1W88 1W88] (E1 in complex with subunit binding domain of E2, ''Geobacillus stearothermophilus''), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2PDE 2PDE] (peripheral subunit binding domain, ''Geobacillus stearothermophilus''), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1LAC 1LAC] (lipoyl domain, ''Geobacillus stearothermophilus''), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1B5S 1B5S] (catalytic domain (residues 184-425) , ''Geobacillus stearothermophilus'')

@@ Line 43: / Line 43: @@
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[carbon core metabolism]]}},
-{{SubtiWiki category|[[membrane proteins]]}}
+{{SubtiWiki category|[[membrane proteins]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 65: / Line 66: @@
 === Additional information===
 =The protein=
@@ Line 83: / Line 81: @@
 * '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:''' phosphorylated (Ser/Thr/Tyr) [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 ** lipoic acid
@@ Line 128: / Line 126: @@
 * '''Regulatory mechanism:'''
 ** stringent response: due to presence of guanine at +1 position of the transcript {{PubMed|20081037}}
 =Biological materials =
@@ Line 153: / Line 152: @@
 <pubmed> 19476487 9655937 2227213 6805383 1794583 </pubmed>
 ==Original publications==
-<pubmed>9352926,, 9352926,17726680 ,12850135 18763711 6414463 11976308 20081037 22862776 </pubmed>
+<pubmed>9352926,, 9352926,17726680 ,12850135 18763711 6414463 11976308 20081037 22862776 15378759</pubmed>
 [[Category:Protein-coding genes]]

@@ 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=PdhC PdhC]
 |-
-|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=pdhC pdhC]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 4.855

@@ 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=BSU14600 pdhC]
 |-
-|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/PdhC PdhC]
+|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=PdhC PdhC]
 |-
 |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 88: / Line 88: @@
 * '''Cofactor(s):'''
 * '''Effectors of protein activity:'''
-** Inhibited thiamine 2-thiothiazolone diphosphate and NADH [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]
+** Inhibited by thiamine 2-thiothiazolone diphosphate and NADH [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]
 ** Low sensibility to NADPH

@@ Line 39: / Line 39: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 81: / Line 77: @@
 * '''Protein family:''' lipoyl-binding domain (according to Swiss-Prot)
-* '''Paralogous protein(s):'''
+* '''Paralogous protein(s):''' [[AcoC]], [[BkdB]], [[OdhB]]
 === Extended information on the protein ===
@@ Line 121: / Line 117: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pdhC_1530537_1531865_1 pdhC] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 ** ''[[pdhA]]'': [[SigA]] {{PubMed|20081037}}
 ** ''[[pdhC]]'': [[SigA]] {{PubMed|11976308}}