PtkA - Revision history

Jstuelk: /* Reviews */

2015-08-20T12:51:18Z

‎Reviews

Jstuelk at 17:06, 19 August 2015

2015-08-19T17:06:03Z

Jstuelk: /* Reviews */

2015-02-11T11:33:04Z

‎Reviews

Jstuelk: /* Reviews */

2015-01-02T10:54:16Z

‎Reviews

Jstuelk: /* Original publications */

2014-11-07T10:05:20Z

‎Original publications

Jstuelk: /* Original publications */

2014-10-04T15:48:29Z

‎Original publications

Jstuelk: /* Reviews */

2014-05-28T13:52:48Z

‎Reviews

Jstuelk: /* Original publications */

2014-04-15T07:12:04Z

‎Original publications

134.76.38.147 at 14:59, 2 April 2014

2014-04-02T14:59:46Z

Jstuelk: /* Original publications */

2014-02-06T12:01:03Z

‎Original publications

← Older revision		Revision as of 12:51, 20 August 2015
Line 1:		Line 1:
−	* '''Description:~~''' [[protein kinases and phosphatases\|protein tyrosine kinase]] <br/><br/>~~	+	{{#bank: PtkA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''ptkA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ywqD ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| [[protein kinases and phosphatases\|protein tyrosine kinase]]~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| protein phosphorylation~~
−	\|-
−	\|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=BSU36250 ptkA]
−	\|-
−	\|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=PtkA PtkA]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 25 kDa, 9.628~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 711 bp, 237 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ptpZ]]'', ''[[tkmA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU36250 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU36250 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU36250 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ywqD_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=ptkA_3731822_3732535_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ptkA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36250]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[biofilm formation]]}},~~
−	~~{{SubtiWiki category\|[[protein modification]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[AbrB regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[DegU regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[Spo0A regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU36250
−
−	~~===Phenotypes of a mutant ===~~
−	* Accumulation of extra chromosome equivalents [http://www.ncbi.nlm.nih.gov/sites/entrez/17367396 PubMed]
−	* Defect in [[biofilm formation]], this involves the kinase activity, but the target protein is unknown {{PubMed\|20815827}}
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU36250&redirect=T BSU36250]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ywqCD.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12508]
−
−	~~=== 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), autophosphorylation, phosphorylation of [[Ugd]], [[TuaD]], [[Ssb]], [[SsbB]]
−
−	* '''Protein family:''' BY-kinase, see the [http://bykdb.ibcp.fr/BYKdb/BYKdbHelp Bacterial Protein Tyrosine Kinase Database])
−
−	* '''Paralogous protein(s):''' [[EpsB]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:''' single BY-kinase domain
−
−	* '''Modification:''' autophosphorylation at residues Y225, Y227 and Y228 (primary site) {{PubMed\|20509597}}, dephosphorylated by [[PtpZ]] {{PubMed\|15866923}}
−
−	* '''[[Cofactors]]:''' ATP
−
−	* '''Effectors of protein activity:''' [[TkmA]] - transmembrane modulator, activates PtkA autophosphorylation and substrate phosphorylation [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[PtkA]]-[[TkmA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
−	** [[FatR]]-[[PtkA]] {{PubMed\|23939619}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU36250&redirect=T BSU36250]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2VED 2VED] (CapB, the homolog in ''Staphylococcus aureus'')
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P96716 P96716]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU36250]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' ''[[tkmA]]-[[ptkA]]-[[ptpZ]]-[[ugd]]'' {{PubMed\|20815827,12970183}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ptkA_3731822_3732535_-1 ptkA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|20815827}}
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−	** [[Spo0A]]: transcription activation {{PubMed\|26283769}}
−	** [[DegU]]-P: transcription activation {{PubMed\|26283769}}
−	** [[AbrB]]: transcription repression {{PubMed\|20817675}}
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** KO strain created with pMUTIN-2, available from [[Ivan Mijakovic]]
−	** GP1520 (spc), available in [[ Jörg Stülke]]'s lab
−	** GP1544 (ermC), available in [[ Jörg Stülke]]'s lab
−	** GP1587 (cat) , available in [[ Jörg Stülke]]'s lab
−	** GP1521 ''[[epsB]]'' (aphA3) ''[[ptkA]]'' (spc) double mutant available in [[ Jörg Stülke]]'s lab
−	** GP1529 ''[[tkmA]]-[[ptkA]]''::spc available in [[ Jörg Stülke]]'s lab
−	** GP1610 (''[[ptkA]]-[[ptpZ]]'', spc), available in [[ Jörg Stülke]]'s lab
−
−	* '''Expression vector:''' pQE-30, N-terminally 6xHis-tagged, available from [[Ivan Mijakovic]]
−
−	* '''lacZ fusion:''' in a KO strain created with pMUTIN-2, available from [[Ivan Mijakovic]]
−
−	* '''GFP fusion:''' CFP-fusion, available from [[Ivan Mijakovic]]
−
−	* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[ Jörg Stülke]]'s lab
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−	~~[[Ivan Mijakovic]], Thiverval-Grignon, France~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed> 20497498 24554699 25540643 25667587</pubmed>~~
−
−	~~==Original publications==~~
−	~~<pubmed> 12970183, 15741737, 15866923, 17367396, 19258708 18547145 20497499 20509597 20815827 20817675 23939619 24493247 24728941 25278935 25374563 26283769</pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

@@ Line 45: / Line 45: @@
 = This gene is a member of the following [[regulons]] =
-{{SubtiWiki regulon|[[AbrB regulon]]}}
+{{SubtiWiki regulon|[[AbrB regulon]]}},
 =The gene=
@@ Line 116: / Line 118: @@
 * '''Regulatory mechanism:'''
-** [[DegU]]-P: transcription repression {{PubMed|20815827}}
+** [[Spo0A]]: transcription activation {{PubMed|26283769}}
 ** [[AbrB]]: transcription repression {{PubMed|20817675}}
@@ Line 152: / Line 155: @@
 ==Original publications==
-<pubmed> 12970183, 15741737, 15866923, 17367396, 19258708 18547145 20497499 20509597 20815827 20817675 23939619 24493247 24728941 25278935 25374563 </pubmed>
+<pubmed> 12970183, 15741737, 15866923, 17367396, 19258708 18547145 20497499 20509597 20815827 20817675 23939619 24493247 24728941 25278935 25374563 26283769</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 149: / Line 149: @@
 =References=
 ==Reviews==
-<pubmed> 20497498 24554699 25540643</pubmed>
+<pubmed> 20497498 24554699 25540643 25667587</pubmed>
 ==Original publications==
 <pubmed> 12970183, 15741737, 15866923, 17367396, 19258708 18547145 20497499 20509597 20815827 20817675 23939619 24493247 24728941 25278935 25374563 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 149: / Line 149: @@
 =References=
 ==Reviews==
-<pubmed> 20497498 24554699 </pubmed>
+<pubmed> 20497498 24554699 25540643</pubmed>
 ==Original publications==
 <pubmed> 12970183, 15741737, 15866923, 17367396, 19258708 18547145 20497499 20509597 20815827 20817675 23939619 24493247 24728941 25278935 25374563 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 152: / Line 152: @@
 ==Original publications==
-<pubmed> 12970183, 15741737, 15866923, 17367396, 19258708 18547145 20497499 20509597 20815827 20817675 23939619 24493247 24728941 25278935 </pubmed>
+<pubmed> 12970183, 15741737, 15866923, 17367396, 19258708 18547145 20497499 20509597 20815827 20817675 23939619 24493247 24728941 25278935 25374563 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 151: / Line 151: @@
 <pubmed> 20497498 </pubmed>
 ==Original publications==
-<pubmed> 12970183, 15741737, 15866923, 17367396, 19258708 18547145 20497499 20509597 20815827 20817675 23939619 24493247 </pubmed>
+<pubmed> 12970183, 15741737, 15866923, 17367396, 19258708 18547145 20497499 20509597 20815827 20817675 23939619 24493247 24728941 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 57: / Line 57: @@
 * Defect in [[biofilm formation]], this involves the kinase activity, but the target protein is unknown {{PubMed|20815827}}
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ywqCD.html]
@@ Line 93: / Line 94: @@
 === Database entries ===
 * '''Structure:'''	[http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2VED 2VED] (CapB, the homolog in ''Staphylococcus aureus'')