PdhD - Revision history

Jstuelk: /* Reviews */

2014-05-28T13:51:49Z

‎Reviews

134.76.70.252 at 14:11, 17 April 2014

2014-04-17T14:11:34Z

134.76.70.252 at 09:40, 17 April 2014

2014-04-17T09:40:39Z

134.76.38.147 at 13:36, 2 April 2014

2014-04-02T13:36:52Z

Jstuelk at 13:21, 5 March 2014

2014-03-05T13:21:39Z

Jstuelk: /* Reviews */

2014-02-17T12:35:40Z

‎Reviews

Jstuelk: /* Reviews */

2014-02-17T12:35:24Z

‎Reviews

134.76.70.252 at 10:41, 7 January 2014

2014-01-07T10:41:23Z

Jstuelk: /* Original publications */

2013-11-17T16:35:50Z

‎Original publications

134.76.70.252 at 16:10, 11 November 2013

2013-11-11T16:10:25Z

← Older revision		Revision as of 13:51, 28 May 2014
Line 1:		Line 1:
−	* '''Description:~~''' dihydrolipoamide dehydrogenase E3 subunit of both pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase complexes <br/><br/>~~	+	{{#bank: PdhD}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''pdhD''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''citL ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| dihydrolipoamide dehydrogenase E3 subunit<br/> of both pyruvate dehydrogenase and 2-oxoglutarate<br/> dehydrogenase complexes~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| links glycolysis and TCA cycle, enzyme in 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=BSU14610 pdhD]
−	\|-
−	\|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=PdhD PdhD]
−	\|-
−	\|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=pdhD pdhD]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 49 kDa, 4.76~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1410 bp, 470 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[pdhC]]'', ''[[slp]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU14610 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU14610 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU14610 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:pdhD_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=pdhD_1531870_1533282_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:pdhD_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14610]]
−	\|-
−	\|}
−
−	~~__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]]}},~~
−	~~[[most abundant proteins]]~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[stringent response]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU14610
−
−	~~===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=BSU14610&redirect=T BSU14610]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pdhABCD.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10210]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' Protein N(6)-(dihydrolipoyl)lysine + NAD<sup>+</sup> = protein N(6)-(lipoyl)lysine + NADH (according to Swiss-Prot)
−
−	* '''Protein family:''' class-I pyridine nucleotide-disulfide oxidoreductase family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):''' [[AcoL]], [[LpdV]]
−
−	~~=== 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]]:'''
−
−	* '''Effectors of protein activity:'''
−	** Inhibited thiamine 2-thiothiazolone diphosphate and NADH [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]
−	** Low sensibility to NADPH [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[OdhA]]-[[OdhB]]-[[PdhD]] {{PubMed\|20933603}}
−	** [[PdhA]]-[[PdhB]]-[[PdhC]]-[[PdhD]]
−
−	* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU14610&redirect=T BSU14610]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1EBD 1EBD] (complex with binding domain of dihydrolipoamide acetylase, Geobacillus stearothermophilus), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EBD 1EBD] (complex with binding domain of dihydrolipoamide acetylase, ''Geobacillus stearothermophilus'')
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P21880 P21880]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14610]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/1.8.1.4 1.8.1.4]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	** ''[[pdhA]]-[[pdhB]]-[[pdhC]]-[[pdhD]]'' {{PubMed\|11976308}}
−	** ''[[pdhC]]-[[pdhD]]'' {{PubMed\|11976308}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pdhD_1531870_1533282_1 pdhD] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−	** ''[[pdhA]]'': [[SigA]] {{PubMed\|20081037}}
−	** ''[[pdhC]]'': [[SigA]] {{PubMed\|11976308}}
−
−	* '''Regulation:'''
−	** ''[[pdhA]]'': expression activated by glucose (2.0-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}}
−
−	* '''Additional information:'''
−	** belongs to the 100 [[most abundant proteins]] {{PubMed\|15378759}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 11483 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 30290 {{PubMed\|24696501}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 11794 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 8779 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 6741 {{PubMed\|21395229}}
−
−	~~=Biological materials =~~
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:''' pGP723 (in [[pAC5]]), available in [[Stülke]] lab
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
−
−	* '''Antibody:'''
−
−	* '''FLAG-tag construct:''' GP1427 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed> 19476487 9655937 2227213 6805383 10672230 </pubmed>~~
−
−	~~==Original publications==~~
−	~~<pubmed>12850135 6414463 11976308 17726680 20081037 20933603 24204596 15378759</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 135: / Line 135: @@
 ** number of protein molecules per cell (minimal medium with glucose and ammonium): 11483 {{PubMed|24696501}}
 ** number of protein molecules per cell (complex medium with amino acids, without glucose): 30290 {{PubMed|24696501}}
 =Biological materials =
 * '''Mutant:'''

@@ Line 133: / Line 133: @@
 * '''Additional information:'''
 ** belongs to the 100 [[most abundant proteins]] {{PubMed|15378759}}
 =Biological materials =

@@ Line 59: / Line 59: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pdhABCD.html]
@@ Line 100: / Line 101: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1EBD 1EBD] (complex with binding domain of dihydrolipoamide acetylase, Geobacillus stearothermophilus),  [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EBD 1EBD] (complex with binding domain of dihydrolipoamide acetylase, ''Geobacillus stearothermophilus'')

@@ Line 42: / Line 42: @@
 = [[Categories]] containing this gene/protein =
-{{SubtiWiki category|[[carbon core metabolism]]}}
+{{SubtiWiki category|[[carbon core metabolism]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 82: / Line 83: @@
 * '''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]]:'''
 * '''Effectors of protein activity:'''
@@ Line 117: / Line 118: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pdhD_1531870_1533282_1 pdhD] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 ** ''[[pdhA]]'': [[SigA]] {{PubMed|20081037}}
 ** ''[[pdhC]]'': [[SigA]] {{PubMed|11976308}}
@@ Line 129: / Line 130: @@
 * '''Additional information:'''
 =Biological materials =
@@ Line 155: / Line 157: @@
 ==Original publications==
-<pubmed>12850135 6414463 11976308 17726680 20081037 20933603  24204596</pubmed>
+<pubmed>12850135 6414463 11976308 17726680 20081037 20933603  24204596 15378759</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 152: / Line 152: @@
 =References=
 ==Reviews==
-<pubmed> 19476487 9655937 2227213 6805383 10672230 22340847 </pubmed>
+<pubmed> 19476487 9655937 2227213 6805383 10672230 </pubmed>
 ==Original publications==

@@ 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=PdhD PdhD]
 |-
-|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=pdhD pdhD]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 4.76

@@ 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=BSU14610 pdhD]
 |-
-|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/PdhD PdhD]
+|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=PdhD PdhD]
 |-
 |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]'''