AbrB - Revision history

Jstuelk: /* Other original publications */

2015-03-20T11:46:04Z

‎Other original publications

Jstuelk: /* Other original publications */

2014-11-10T09:27:32Z

‎Other original publications

Jstuelk at 07:59, 14 October 2014

2014-10-14T07:59:46Z

Jstuelk: /* Other original publications */

2014-07-10T12:27:14Z

‎Other original publications

Jstuelk: /* Other original publications */

2014-05-18T14:16:23Z

‎Other original publications

134.76.70.252 at 09:47, 17 April 2014

2014-04-17T09:47:56Z

Jstuelk at 10:29, 16 April 2014

2014-04-16T10:29:09Z

134.76.38.147 at 12:46, 2 April 2014

2014-04-02T12:46:04Z

Jstuelk: /* Other original publications */

2014-02-19T08:09:22Z

‎Other original publications

Jstuelk at 08:08, 19 February 2014

2014-02-19T08:08:49Z

← Older revision		Revision as of 11:46, 20 March 2015
Line 1:		Line 1:
−	* '''Description:~~''' transcriptional regulator of transition state genes <br/><br/>~~	+	{{#bank: AbrB}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''abrB''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''cpsX, tolB ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| transcriptional regulator~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| regulation of gene expression during the transition <br/>from growth to stationary phase~~
−	\|-
−	\|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=BSU00370 abrB]
−	\|-
−	\|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=AbrB AbrB]
−	\|-
−	\|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=abrB abrB]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 10 kDa, 6.57~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 282 bp, 94 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yabC]]'', ''[[metS]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00370 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00370 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00370 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:abrB_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=abrB_44848_45138_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:abrB_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00370]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[transition state regulators]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[AbrB regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[Spo0A regulon]]}}~~
−	~~=The [[AbrB regulon]]=~~
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU00370
−
−	~~===Phenotypes of a mutant ===~~
−	* No swarming motility on B medium [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00370&redirect=T BSU00370]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/abrB.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10100]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):''' [[Abh]], [[SpoVT]] (only N-terminal domain)
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:''' phosphorylated on Ser-86 {{PubMed\|20509597}} by [[PrkC]], [[PrkD]], and [[YabT]] results in loss of DNA-binding activity {{PubMed\|24731262}}
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:''' interaction with [[AbbA]] results in inactivation of AbrB [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[AbbA]]-[[AbrB]], [[AbbA]] binds the N-terminal DNA-binding domain of [[AbrB]] {{PubMed\|24534728,18840696}}
−	** [[AbrB]]-[[AbrB]] {{PubMed\|20817675}}
−	** [[AbrB]]-[[Abh]] {{PubMed\|20817675}}
−	** [[AbrB]]-[[PrkC]] {{PubMed\|24731262}}
−	** [[AbrB]]-[[PrkD]] {{PubMed\|24731262}}
−	** [[AbrB]]-[[YabT]] {{PubMed\|24731262}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00370&redirect=T BSU00370]
−
−	* '''Structure:'''
−	** [http://www.rcsb.org/pdb/explore.do?structureId=1Z0R 1Z0R] (N-terminal DNA recognition domain), [http://www.ncbi.nlm.nih.gov/sites/entrez/16223496 PubMed]
−	** [http://www.rcsb.org/pdb/explore.do?structureId=2MJG 2MJG] (full-length protein) {{PubMed\|25308864}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P08874 P08874]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00370]
−
−	~~=== Additional information===~~
−
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''abrB'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=abrB_44848_45138_-1 abrB] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
−
−	* '''Regulation:''' expressed at the onset of stationary phase [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
−	** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/2106683,15687200 PubMed]
−	** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/2504584 PubMed]
−
−	* '''Regulatory mechanism:''' repressed by [[Spo0A]]-P [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
−	** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/2106683,15687200 PubMed]
−	** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/2504584 PubMed]
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 2859 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 10811 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:''' TT731 (aphA3)
−	** 1A935 (''abrB''::''cat''), {{PubMed\|11886552}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A935&Search=1A935 BGSC]
−	** GP1548 (''abrB''::''ermC''), available in [[Stülke]] lab
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''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=~~
−
−	~~[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]~~
−
−	~~[[Mark Strauch]], Baltimore, USA [http://lifesciences.umaryland.edu/Pages/faculty_profile.aspx?ID=212 homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>11964117 19995980 11931565 19202088,18326573</pubmed>~~
−	~~==The [[AbrB regulon]]: ==~~
−	~~<pubmed>20817675,18840696 23580539</pubmed>~~
−	~~==Other original publications==~~
−	<pubmed> 19581368 ,3145384,2437099,8878039,2504584, 11377867,1850083,2106683,12586407, 12076816,17660417, 2554317,18430133,7768874, 2507867, 1766371, 15687200,1908787,2106683,15687200, 2504584,3145384 8821944 8576231 11101897 11395475 11583849 11751836 12123659 12076816 12591885 15610005 16223496 16159768 16702211 17660417 17720793 7592460, 19465659 20509597 15101989 19202088,18326573 24534728 24731262 24832089 25002359 25308864 25381239 </pubmed>
−	~~[[Category:Protein-coding genes]]~~

@@ Line 162: / Line 162: @@
 <pubmed>20817675,18840696 23580539</pubmed>
 ==Other original publications==
-<pubmed> 19581368 ,3145384,2437099,8878039,2504584, 11377867,1850083,2106683,12586407, 12076816,17660417, 2554317,18430133,7768874, 2507867, 1766371, 15687200,1908787,2106683,15687200, 2504584,3145384 8821944 8576231 11101897 11395475 11583849 11751836 12123659 12076816 12591885 15610005 16223496 16159768 16702211 17660417 17720793 7592460, 19465659  20509597 15101989 19202088,18326573 24534728 24731262 24832089 25002359 25308864 </pubmed>
+<pubmed> 19581368 ,3145384,2437099,8878039,2504584, 11377867,1850083,2106683,12586407, 12076816,17660417, 2554317,18430133,7768874, 2507867, 1766371, 15687200,1908787,2106683,15687200, 2504584,3145384 8821944 8576231 11101897 11395475 11583849 11751836 12123659 12076816 12591885 15610005 16223496 16159768 16702211 17660417 17720793 7592460, 19465659  20509597 15101989 19202088,18326573 24534728 24731262 24832089 25002359 25308864 25381239 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 101: / Line 101: @@
 * '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00370&redirect=T BSU00370]
-* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1Z0R 1Z0R] (N-terminal DNA recognition domain), [http://www.ncbi.nlm.nih.gov/sites/entrez/16223496 PubMed]
+* '''Structure:'''
 * '''UniProt:''' [http://www.uniprot.org/uniprot/P08874 P08874]
@@ Line 160: / Line 162: @@
 <pubmed>20817675,18840696 23580539</pubmed>
 ==Other original publications==
-<pubmed> 19581368 ,3145384,2437099,8878039,2504584, 11377867,1850083,2106683,12586407, 12076816,17660417, 2554317,18430133,7768874, 2507867, 1766371, 15687200,1908787,2106683,15687200, 2504584,3145384 8821944 8576231 11101897 11395475 11583849 11751836 12123659 12076816 12591885 15610005 16223496 16159768 16702211 17660417 17720793 7592460, 19465659  20509597 15101989 19202088,18326573 24534728 24731262 24832089 25002359 </pubmed>
+<pubmed> 19581368 ,3145384,2437099,8878039,2504584, 11377867,1850083,2106683,12586407, 12076816,17660417, 2554317,18430133,7768874, 2507867, 1766371, 15687200,1908787,2106683,15687200, 2504584,3145384 8821944 8576231 11101897 11395475 11583849 11751836 12123659 12076816 12591885 15610005 16223496 16159768 16702211 17660417 17720793 7592460, 19465659  20509597 15101989 19202088,18326573 24534728 24731262 24832089 25002359 25308864 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 160: / Line 160: @@
 <pubmed>20817675,18840696 23580539</pubmed>
 ==Other original publications==
-<pubmed> 19581368 ,3145384,2437099,8878039,2504584, 11377867,1850083,2106683,12586407, 12076816,17660417, 2554317,18430133,7768874, 2507867, 1766371, 15687200,1908787,2106683,15687200, 2504584,3145384 8821944 8576231 11101897 11395475 11583849 11751836 12123659 12076816 12591885 15610005 16223496 16159768 16702211 17660417 17720793 7592460, 19465659  20509597 15101989 19202088,18326573 24534728 24731262 24832089 </pubmed>
+<pubmed> 19581368 ,3145384,2437099,8878039,2504584, 11377867,1850083,2106683,12586407, 12076816,17660417, 2554317,18430133,7768874, 2507867, 1766371, 15687200,1908787,2106683,15687200, 2504584,3145384 8821944 8576231 11101897 11395475 11583849 11751836 12123659 12076816 12591885 15610005 16223496 16159768 16702211 17660417 17720793 7592460, 19465659  20509597 15101989 19202088,18326573 24534728 24731262 24832089 25002359 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 160: / Line 160: @@
 <pubmed>20817675,18840696 23580539</pubmed>
 ==Other original publications==
-<pubmed> 19581368 ,3145384,2437099,8878039,2504584, 11377867,1850083,2106683,12586407, 12076816,17660417, 2554317,18430133,7768874, 2507867, 1766371, 15687200,1908787,2106683,15687200, 2504584,3145384 8821944 8576231 11101897 11395475 11583849 11751836 12123659 12076816 12591885 15610005 16223496 16159768 16702211 17660417 17720793 7592460, 19465659  20509597 15101989 19202088,18326573 24534728 24731262</pubmed>
+<pubmed> 19581368 ,3145384,2437099,8878039,2504584, 11377867,1850083,2106683,12586407, 12076816,17660417, 2554317,18430133,7768874, 2507867, 1766371, 15687200,1908787,2106683,15687200, 2504584,3145384 8821944 8576231 11101897 11395475 11583849 11751836 12123659 12076816 12591885 15610005 16223496 16159768 16702211 17660417 17720793 7592460, 19465659  20509597 15101989 19202088,18326573 24534728 24731262 24832089 </pubmed>
 [[Category:Protein-coding genes]]

← Older revision		Revision as of 09:47, 17 April 2014
Line 127:		Line 127:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 2859 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 10811 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 55: / Line 55: @@
 ===Phenotypes of a mutant ===
+* No swarming motility on B medium [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]
 === Database entries ===
@@ Line 83: / Line 82: @@
 * '''[[Domains]]:'''
-* '''Modification:''' phosphorylated on Ser-86 {{PubMed|20509597}}
+* '''Modification:''' phosphorylated on Ser-86 {{PubMed|20509597}} by [[PrkC]], [[PrkD]], and [[YabT]] results in loss of DNA-binding activity {{PubMed|24731262}}
 * '''[[Cofactors]]:'''
@@ Line 93: / Line 92: @@
 ** [[AbrB]]-[[AbrB]] {{PubMed|20817675}}
 ** [[AbrB]]-[[Abh]] {{PubMed|20817675}}
 * '''[[Localization]]:'''
@@ Line 156: / Line 158: @@
 <pubmed>20817675,18840696 23580539</pubmed>
 ==Other original publications==
-<pubmed> 19581368 ,3145384,2437099,8878039,2504584, 11377867,1850083,2106683,12586407, 12076816,17660417, 2554317,18430133,7768874, 2507867, 1766371, 15687200,1908787,2106683,15687200, 2504584,3145384 8821944 8576231 11101897 11395475 11583849 11751836 12123659 12076816 12591885 15610005 16223496 16159768 16702211 17660417 17720793 7592460, 19465659  20509597 15101989 19202088,18326573 24534728 </pubmed>
+<pubmed> 19581368 ,3145384,2437099,8878039,2504584, 11377867,1850083,2106683,12586407, 12076816,17660417, 2554317,18430133,7768874, 2507867, 1766371, 15687200,1908787,2106683,15687200, 2504584,3145384 8821944 8576231 11101897 11395475 11583849 11751836 12123659 12076816 12591885 15610005 16223496 16159768 16702211 17660417 17720793 7592460, 19465659  20509597 15101989 19202088,18326573 24534728 24731262</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 80: / Line 80: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:''' phosphorylated on Ser-86 {{PubMed|20509597}}
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:''' interaction with [[AbbA]] results in inactivation of AbrB [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
 * '''[[SubtInteract|Interactions]]:'''
-** [[AbrB]]-[[AbbA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
+** [[AbbA]]-[[AbrB]], [[AbbA]] binds the N-terminal DNA-binding domain of [[AbrB]] {{PubMed|24534728,18840696}}
 ** [[AbrB]]-[[AbrB]] {{PubMed|20817675}}
 ** [[AbrB]]-[[Abh]] {{PubMed|20817675}}
@@ Line 97: / Line 97: @@
 === Database entries ===
-* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1Z0R 1Z0R] (N-terminal DNA recognition domain), [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=32611 NCBI] [http://www.ncbi.nlm.nih.gov/sites/entrez/16223496 PubMed]
+* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1Z0R 1Z0R] (N-terminal DNA recognition domain), [http://www.ncbi.nlm.nih.gov/sites/entrez/16223496 PubMed]
 * '''UniProt:''' [http://www.uniprot.org/uniprot/P08874 P08874]