PdhB - Revision history

Jstuelk: /* Reviews */

2014-05-28T13:51:32Z

‎Reviews

134.76.70.252 at 14:11, 17 April 2014

2014-04-17T14:11:27Z

134.76.70.252 at 09:41, 17 April 2014

2014-04-17T09:41:32Z

134.76.38.147 at 13:36, 2 April 2014

2014-04-02T13:36:43Z

Jstuelk at 16:02, 5 March 2014

2014-03-05T16:02:25Z

134.76.70.252 at 10:41, 7 January 2014

2014-01-07T10:41:16Z

134.76.70.252 at 16:10, 11 November 2013

2013-11-11T16:10:16Z

Jstuelk: /* Basic information/ Evolution */

2013-06-08T19:08:41Z

‎Basic information/ Evolution

Jstuelk: /* Basic information/ Evolution */

2013-06-08T19:08:14Z

‎Basic information/ Evolution

134.76.70.252 at 13:10, 16 May 2013

2013-05-16T13:10:59Z

← Older revision		Revision as of 13:51, 28 May 2014
Line 1:		Line 1:
−	* '''Description:~~''' pyruvate dehydrogenase (E1 beta subunit) <br/><br/>~~	+	{{#bank: PdhB}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''pdhB''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| pyruvate dehydrogenase (E1 beta 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=BSU14590 pdhB]
−	\|-
−	\|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=PdhB PdhB]
−	\|-
−	\|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=pdhB pdhB]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 35 kDa, 4.547~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 975 bp, 325 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[pdhA]]'', ''[[pdhC]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU14590 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU14590 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU14590 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:pdhB_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=pdhB_1529445_1530422_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:pdhB_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14590]]
−	\|-
−	\|}
−
−	~~__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]]}},~~
−	~~{{SubtiWiki category\|[[phosphoproteins]]}},~~
−	~~[[most abundant proteins]]~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[stringent response]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU14590
−
−	~~===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=BSU14590&redirect=T BSU14590]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pdhABCD.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10208]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' Pyruvate + [dihydrolipoyllysine-residue acetyltransferase] lipoyllysine = [dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine + CO<sub>2</sub> (according to Swiss-Prot)
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):''' [[AcoB]], [[BkdAB]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:''' phosphorylation on (Ser-302 OR Ser-306) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 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
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[PdhA]]-[[PdhB]]-[[PdhC]]-[[PdhD]]
−
−	* '''[[Localization]]:''' membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU14590&redirect=T BSU14590]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1W88 1W88] (E1 in complex with subunit binding domain of E2, ''Geobacillus stearothermophilus'')
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P21882 P21882]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14590]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.4.1 1.2.4.1]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[pdhA]]-[[pdhB]]-[[pdhC]]-[[pdhD]]'' {{PubMed\|11976308}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pdhB_1529445_1530422_1 pdhB] {{PubMed\|22383849}}
−
−	* '''Sigma factor:''' [[SigA]] {{PubMed\|20081037}}
−
−	* '''Regulation:'''
−	** expression activated by glucose (2.8-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): 10912 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 30160 {{PubMed\|24696501}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 10905 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 6526 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 6489 {{PubMed\|21395229}}
−
−	~~=Biological materials =~~
−	* '''Mutant:''' GP459 (spc), available in [[Stülke]] lab
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:''' pGP722 (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:'''
−
−	~~=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 </pubmed>~~
−	~~==Original publications==~~
−	~~<pubmed>9352926,15378759,12850135 17218307 18763711 6414463 11976308 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 129: / Line 129: @@
 ** number of protein molecules per cell (minimal medium with glucose and ammonium): 10912 {{PubMed|24696501}}
 ** number of protein molecules per cell (complex medium with amino acids, without glucose): 30160 {{PubMed|24696501}}
 =Biological materials =
 * '''Mutant:''' GP459 (spc), available in [[Stülke]] lab

@@ Line 127: / Line 127: @@
 * '''Additional information:'''
 ** 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 97: / Line 98: @@
 === 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'')

@@ Line 39: / Line 39: @@
 <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]]}},
-{{SubtiWiki category|[[phosphoproteins]]}}
+{{SubtiWiki category|[[phosphoproteins]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 69: / Line 66: @@
 === Additional information===
 =The protein=
@@ Line 87: / Line 81: @@
 * '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:''' phosphorylation on (Ser-302 OR Ser-306) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 130: / Line 124: @@
 * '''Additional information:'''
 =Biological materials =
@@ Line 155: / Line 150: @@
 <pubmed> 19476487 9655937 2227213 6805383 </pubmed>
 ==Original publications==
-<pubmed>9352926,,12850135 17218307 18763711 6414463 11976308</pubmed>
+<pubmed>9352926,15378759,12850135 17218307 18763711 6414463 11976308 </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=PdhB PdhB]
 |-
-|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=pdhB pdhB]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35 kDa, 4.547

@@ 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=BSU14590 pdhB]
 |-
-|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/PdhB PdhB]
+|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=PdhB PdhB]
 |-
 |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 81: / Line 81: @@
 * '''Protein family:'''
-* '''Paralogous protein(s):''' [[PdhB]], [[AcoB]], [[BkdAB]]
+* '''Paralogous protein(s):''' [[AcoB]], [[BkdAB]]
 === Extended information on the protein ===

@@ Line 31: / Line 31: @@
   <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=pdhB_1529445_1530422_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:pdhB_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pdhB_1529445_1530422_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:pdhB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14590]]
 |-
 |}