KinD - Revision history

Jstuelk at 15:40, 28 August 2015

2015-08-28T15:40:01Z

134.76.38.147 at 13:33, 2 April 2014

2014-04-02T13:33:01Z

134.76.70.252 at 10:37, 7 January 2014

2014-01-07T10:37:58Z

134.76.70.252 at 16:07, 11 November 2013

2013-11-11T16:07:04Z

134.76.70.252 at 13:07, 16 May 2013

2013-05-16T13:07:00Z

134.76.70.252 at 10:02, 14 May 2013

2013-05-14T10:02:58Z

134.76.70.252 at 12:40, 13 May 2013

2013-05-13T12:40:13Z

Jstuelk at 10:52, 15 April 2013

2013-04-15T10:52:23Z

Jstuelk at 12:11, 26 February 2013

2013-02-26T12:11:13Z

Jstuelk at 11:50, 26 February 2013

2013-02-26T11:50:12Z

← Older revision		Revision as of 15:40, 28 August 2015
Line 1:		Line 1:
−	* '''Description:''' osmo-sensing [[two-component systems\|two-component]] sensor [[protein kinases and phosphatases\|kinase]], phosphorylates [[Spo0F]], part of the [[phosphorelay]], checkpoint protein that links [[sporulation]] initiation to [[biofilm formation]] <br/><br/>	+	{{#bank: KinD}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''kinD''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ykvD ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| [[two-component systems\|two-component]] sensor kinase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| initiation of sporulation~~
−	\|-
−	\|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=BSU13660 kinD]
−	\|-
−	\|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=KinD KinD]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Function and regulation of this protein in [[SubtiPathways\|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=kinD kinD]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 56 kDa, 6.745~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1518 bp, 506 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[eag]]'', ''[[mhqR]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU13660 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU13660 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU13660 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:kinD_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=kinD_1431486_1433006_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:kinD_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU13660]]
−	\|-
−	\|}
−
−	~~__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\|[[transcription factors and their control]]}},~~
−	~~{{SubtiWiki category\|[[phosphorelay]]}},~~
−	~~{{SubtiWiki category\|[[biofilm formation]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}},~~
−	~~{{SubtiWiki category\|[[phosphoproteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU13660
−
−	~~===Phenotypes of a mutant ===~~
−	* deletion of ''kinD'' suppresses the [[sporulation]] defect of matrix mutants, while its overproduction delays [[sporulation]] {{PubMed\|20689749}}
−	* inactivation of ''[[kinD]]'' restores beta-lactam resistance in a ''[[sigM]]'' mutant {{PubMed\|22211522}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU13660&redirect=T BSU13660]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13309]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** autophosphorylation, phosphorylation of [[Spo0F]], regulates the onset of sporulation by inhibiting the activity of [[Spo0A]] until matrix, or a component therein, is sensed [http://mbio.asm.org/content/1/1/e00035-10.full PubMed]
−	** dual role as a [[protein kinases and phosphatases\|phosphatase]] or a [[protein kinases and phosphatases\|kinase]], activity is linked to the presence of extracellular matrix in the biofilms {{PubMed\|20689749}}
−	** mainly active in the younger, outer regions of a colony (with [[KinC]]) {{PubMed\|21097618}}
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−	** two transmembrane segments, between them the extracellular pyruvate-binding sensing domain that consists of tandem PAS-like domains {{PubMed\|23436677,22716461}}
−	** C-terminal histidine phosphotransferase domain
−	** see {{PubMed\|22716461}} for a scheme of the domain organization
−
−	* '''Modification:''' autophosphorylation on a His residue
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−	** activity is stimulated by direct or indirect interaction with [[Med]] {{PubMed\|21622736}}
−	** L-malate seems to trigger KinD activity {{PubMed\|22716461}}, but this effect may be indirect due to the excretion of pyruvate that directly binds the extracytoplasmic sensing domain of KinD {{PubMed\|23436677}}
−	** kinase activity is triggered and phosphatase activity is decreased by increased osmotic pressure {{PubMed\|22882172}}
−	** activity is triggered in the presence of glycerol + manganese {{PubMed\|23564171}}
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[KinD]]-[[Spo0F]]
−
−	* '''[[Localization]]:''' membrane
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU13660&redirect=T BSU13660]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=4DBJ 4DBJ] (extracytoplasmic sensing domain) {{PubMed\|23436677}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O31671 O31671]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13660]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:'''
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=kinD_1431486_1433006_-1 kinD] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed>10094672,11069677,20689749 , 21097618 22074846 22716461 22882172 23436677 23564171 21622736,22211522</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 63: / Line 63: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 108: / Line 109: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=4DBJ 4DBJ] (extracytoplasmic sensing domain) {{PubMed|23436677}}

@@ 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=KinD KinD]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/phosphorelay.html Phosphorelay]'''
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=kinD kinD]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 6.745

@@ 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=BSU13660 kinD]
 |-
-|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/KinD KinD]
+|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=KinD KinD]
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/phosphorelay.html Phosphorelay]'''

@@ 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=kinD_1431486_1433006_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:kinD_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=kinD_1431486_1433006_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:kinD_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU13660]]
 |-
 |}

@@ Line 26: / Line 26: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[eag]]'', ''[[mhqR]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU13660 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU13660 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU13660 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU13660 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU13660 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU13660 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:kinD_context.gif]]

@@ Line 1: / Line 1: @@
-* '''Description:''' osmo-sensing [[two-component systems|two-component]] sensor [[protein kinases and phosphatases|kinase]], phosphorylates [[Spo0F]], part of the [[phosphorelay]], checkpoint protein that links sporulation initiation to [[biofilm formation]] <br/><br/>
+* '''Description:''' osmo-sensing [[two-component systems|two-component]] sensor [[protein kinases and phosphatases|kinase]], phosphorylates [[Spo0F]], part of the [[phosphorelay]], checkpoint protein that links [[sporulation]] initiation to [[biofilm formation]] <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 100: / Line 100: @@
 ** L-malate seems to trigger KinD activity {{PubMed|22716461}}, but this effect may be indirect due to the excretion of pyruvate that directly binds the extracytoplasmic sensing domain of KinD {{PubMed|23436677}}
 ** kinase activity is triggered and phosphatase activity is decreased by increased osmotic pressure {{PubMed|22882172}}
 * '''[[SubtInteract|Interactions]]:'''
@@ Line 151: / Line 152: @@
 =References=
-'''Additonal publications:''' {{PubMed|21622736,22211522}}
+<pubmed>10094672,11069677,20689749 , 21097618   22074846 22716461 22882172 23436677 23564171 21622736,22211522</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 88: / Line 88: @@
 * '''Domains:'''
-** two transmembrane segments, between them the extracellular CACHE domain for L-malate binding {{PubMed|22716461}}
+** two transmembrane segments, between them the extracellular pyruvate-binding sensing domain that consists of tandem PAS-like domains {{PubMed|23436677,22716461}}
 ** C-terminal histidine phosphotransferase domain
 ** see {{PubMed|22716461}} for a scheme of the domain organization
@@ Line 98: / Line 98: @@
 * '''Effectors of protein activity:'''
 ** activity is stimulated by direct or indirect interaction with [[Med]] {{PubMed|21622736}}
-** L-malate seems to trigger KinD activity {{PubMed|22716461}}
+** L-malate seems to trigger KinD activity {{PubMed|22716461}}, but this effect may be indirect due to the excretion of pyruvate that directly binds the extracytoplasmic sensing domain of KinD {{PubMed|23436677}}
 ** kinase activity is triggered and phosphatase activity is decreased by increased osmotic pressure {{PubMed|22882172}}
@@ Line 108: / Line 108: @@
 === Database entries ===
-* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3FOS 3FOS]
+* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=4DBJ 4DBJ] (extracytoplasmic sensing domain) {{PubMed|23436677}}
 * '''UniProt:''' [http://www.uniprot.org/uniprot/O31671 O31671]
@@ Line 152: / Line 152: @@
 =References=
 '''Additonal publications:''' {{PubMed|21622736,22211522}}
-<pubmed>10094672,11069677,20689749 , 21097618   22074846 22716461 22882172 </pubmed>
+<pubmed>10094672,11069677,20689749 , 21097618   22074846 22716461 22882172 23436677 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 39: / Line 39: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 124: / Line 124: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=kinD_1431486_1433006_-1 kinD] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:'''