EpsB - Revision history

Jstuelk: /* Extended information on the protein */

2015-08-19T15:30:41Z

‎Extended information on the protein

Jstuelk: /* Reviews */

2015-01-02T10:54:34Z

‎Reviews

Jstuelk at 09:30, 5 August 2014

2014-08-05T09:30:18Z

Jstuelk at 09:21, 5 August 2014

2014-08-05T09:21:03Z

Jstuelk: /* Reviews */

2014-05-28T13:52:56Z

‎Reviews

Jstuelk: /* Original publications */

2014-04-15T07:12:17Z

‎Original publications

134.76.38.147 at 14:50, 2 April 2014

2014-04-02T14:50:11Z

Jstuelk: /* Biological materials */

2014-02-06T12:55:21Z

‎Biological materials

Jstuelk: /* Original publications */

2014-02-06T12:00:38Z

‎Original publications

JGerwig: /* Biological materials */

2014-01-31T11:36:38Z

‎Biological materials

← Older revision		Revision as of 15:30, 19 August 2015
Line 1:		Line 1:
−	* '''Description:~~''' extracellular polysaccharide synthesis, protein tyrosine kinase <br/><br/>~~	+	{{#bank: EpsB}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''epsB''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yveL ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| protein tyrosine kinase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| [[biofilm formation]]~~
−	\|-
−	\|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=BSU34360 epsB]
−	\|-
−	\|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=EpsB EpsB]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Regulation of this protein in [[SubtiPathways\|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=epsB epsB]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 24 kDa, 9.918~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 681 bp, 227 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[epsC]]'', ''[[epsA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34360 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34360 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34360 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yveL_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=epsB_3528462_3529145_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:epsB_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34360]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[protein modification]]}},~~
−	~~{{SubtiWiki category\|[[biofilm formation]]}},~~
−	~~{{SubtiWiki category\|[[phosphoproteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[AbrB regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[RemA regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SinR regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU34360
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU34360&redirect=T BSU34360]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/eps.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11860]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate (according to Swiss-Prot)
−
−	* '''Protein family:''' BY kinase, see the [http://bykdb.ibcp.fr/BYKdb/BYKdbHelp Bacterial Protein Tyrosine Kinase Database])
−
−	* '''Paralogous protein(s):''' [[PtkA]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:''' autophosphorylated on Tyr-225 and Tyr-227 {{PubMed\|25085422}}
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[EpsA]]-[[EpsB]] (based on [[TkmA]]-[[PtkA]] interaction)
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU34360&redirect=T BSU34360]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2VED 2VED] (CapB, the homolog in ''Staphylococcus aureus'') {{PubMed\|18547145}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P71051 P71051]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34360]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]'' {{PubMed\|15661000}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=epsB_3528462_3529145_-1 epsB] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|15661000}}
−
−	* '''Regulation:'''
−	** repressed by [[SinR]] {{PubMed\|15661000}}
−
−	* '''Regulatory mechanism:'''
−	** [[SinR]]: transcription anti-activation (prevents binding of [[RemA]]) {{PubMed\|23646920}}
−	** [[RemA]]: transcription activation {{PubMed\|23646920}}
−	** [[AbrB]]: transcription repression {{PubMed\|20817675}}
−
−	* '''Additional information:'''
−	** induction by sequestration of [[SinR]] by [[SinI]] or [[SlrA]] {{PubMed\|15661000,19788541}}
−	** the ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]'' operon is not expressed in a ''[[ymdB]]'' mutant {{PubMed\|21856853}}
−	** the amount of the mRNA is substantially decreased upon depletion of [[Rny\|RNase Y]] (this is likely due to the increased stability of the ''[[sinR]]'' mRNA) {{PubMed\|21815947}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** GP1518 (aphA3) {{PubMed\|24493247}}, available in [[ Jörg Stülke]]'s lab
−	** GP1519 (''[[epsA]]-[[epsB]]'', aphA3) {{PubMed\|24493247}}, 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]]) {{PubMed\|24493247}}, available in [[ Jörg Stülke]]'s lab
−
−	* '''Antibody:'''
−
−	* '''FLAG-tag construct:''' GP1541 epsB-FLAG 3x spc (based on [[pGP1331]]) available in [[ Jörg Stülke]]'s lab
−
−	~~=Labs working on this gene/protein=~~
−
−	~~[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>20735481 24554699 25540643</pubmed>~~
−
−	~~==Original publications==~~
−	~~<pubmed>15661000,16430695,18047568,18647168 18547145 20817675 21856853 21815947 23646920 24493247 24728941 25085422 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 154: / Line 154: @@
 =References=
 ==Reviews==
-<pubmed>20735481 24554699 </pubmed>
+<pubmed>20735481 24554699 25540643</pubmed>
 ==Original publications==

@@ Line 1: / Line 1: @@
-* '''Description:''' extracellular polysaccharide synthesis, putative protein tyrosine kinase <br/><br/>
+* '''Description:''' extracellular polysaccharide synthesis, protein tyrosine kinase <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 10: / Line 10: @@
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+|style="background:#ABCDEF;" align="center"| '''Product''' || protein tyrosine kinase
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || [[biofilm formation]]
@@ Line 43: / Line 43: @@
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[protein modification]]}},
-{{SubtiWiki category|[[biofilm formation]]}}
+{{SubtiWiki category|[[biofilm formation]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 83: / Line 84: @@
 * '''[[Domains]]:'''
-* '''Modification:'''
+* '''Modification:''' autophosphorylated on Tyr-225 and Tyr-227 {{PubMed|25085422}}
 * '''[[Cofactors]]:'''

@@ Line 156: / Line 156: @@
 ==Original publications==
-<pubmed>15661000,16430695,18047568,18647168 18547145 20817675 21856853 21815947 23646920 24493247 24728941 </pubmed>
+<pubmed>15661000,16430695,18047568,18647168 18547145 20817675 21856853 21815947 23646920 24493247 24728941 25085422 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 153: / Line 153: @@
 =References=
 ==Reviews==
-<pubmed>20735481 </pubmed>
+<pubmed>20735481 24554699 </pubmed>
 ==Original publications==
 <pubmed>15661000,16430695,18047568,18647168 18547145 20817675 21856853 21815947 23646920 24493247 24728941 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 59: / Line 59: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/eps.html]
@@ Line 94: / Line 95: @@
 === Database entries ===
 * '''Structure:'''	[http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2VED 2VED] (CapB, the homolog in ''Staphylococcus aureus'') {{PubMed|18547145}}

@@ Line 128: / Line 128: @@
 * '''Mutant:'''
-** GP1518 (aphA3), available in [[ Jörg Stülke]]'s lab
+** GP1518 (aphA3) {{PubMed|24493247}}, available in [[ Jörg Stülke]]'s lab
-** GP1519 (''[[epsA]]-[[epsB]]'', aphA3), available in [[ Jörg Stülke]]'s lab
+** GP1519 (''[[epsA]]-[[epsB]]'', aphA3) {{PubMed|24493247}}, available in [[ Jörg Stülke]]'s lab
 * '''Expression vector:'''
@@ Line 137: / Line 137: @@
 * '''GFP fusion:'''
-* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[ Jörg Stülke]]'s lab
+* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]) {{PubMed|24493247}}, available in [[ Jörg Stülke]]'s lab
 * '''Antibody:'''

@@ Line 141: / Line 141: @@
 * '''Antibody:'''
-* '''FLAG-tag construct:''' GP1541 (''[[epsB]]''-3xFLAG ''spc trpC2'') , available in [[Jörg Stülke]]'s lab
+* '''FLAG-tag construct:''' GP1541 epsB-FLAG 3x spc (based on [[pGP1331]]) available in [[ Jörg Stülke]]'s lab
 =Labs working on this gene/protein=