Sda - Revision history

Jstuelk: /* Database entries */

2015-06-01T10:20:35Z

‎Database entries

Jstuelk at 10:20, 1 June 2015

2015-06-01T10:20:17Z

134.76.38.147 at 14:16, 2 April 2014

2014-04-02T14:16:53Z

134.76.70.252 at 11:16, 7 January 2014

2014-01-07T11:16:00Z

134.76.70.252 at 08:54, 12 November 2013

2013-11-12T08:54:58Z

Jstuelk at 17:31, 13 September 2013

2013-09-13T17:31:55Z

134.76.70.252 at 13:59, 16 May 2013

2013-05-16T13:59:01Z

134.76.70.252 at 10:46, 14 May 2013

2013-05-14T10:46:49Z

134.76.70.252 at 13:21, 13 May 2013

2013-05-13T13:21:52Z

134.76.70.252 at 10:45, 20 September 2012

2012-09-20T10:45:34Z

← Older revision		Revision as of 10:20, 1 June 2015
Line 1:		Line 1:
−	* '''Description:~~''' developmental checkpoint protein, inhibits the autokinase activity of [[KinA]] and [[KinB]], control of the [[phosphorelay]]~~	+	{{#bank: Sda}}
−

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''sda''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| developmental checkpoint protein~~
−	\|-
−	\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| mediates a developmental checkpoint coupling<br/>initiation of sporulation (phosphorylation of [[Spo0A]])<br/>to the function of replication initiation proteins
−	\|-
−	\|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=BSU25690 sda]
−	\|-
−	\|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=Sda Sda]
−	\|-
−	\|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=sda sda]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 6 kDa, 5.605~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 156 bp, 52 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yloV]]'', ''[[yqeF]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU25690 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU25690 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU25690 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:sda_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=sda_2647456_2647614_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:sda_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU25690]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[phosphorelay]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[DnaA regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[LexA regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU25690
−
−	~~===Phenotypes of a mutant ===~~
−	*sporulates at a higher frequency
−	*will sporulate in the presence of replication stress
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU25690&redirect=T BSU25690]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sda.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14183]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' Sda is a checkpoint protein that is upregulated in response to replication stress {{PubMed\|11207367}}. Sda inhibits the autokinase activity of [[KinA]] (and likely [[KinB]] as well). This in its turn results in reduced levels of [[Spo0A\|Spo0A~P]]. Thus, replication stressed cells will not initiate sporulation.
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[KinB]]-[[Sda]] {{PubMed\|19465772}}
−	** [[KinA]]-[[Sda]] {{PubMed\|15023339}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU25690&redirect=T BSU25690]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=3D36 3D36] (from Geobacillus stearothermophilus, complex with [[KinB]]) {{PubMed\|19101565}}, [http://www.rcsb.org/pdb/explore.do?structureId=1PV0 1PV0]
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/Q7WY62 Q7WY62]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25690]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−	* [[Sda]] is rapidly degraded by the [[ClpP\|ClpP/X]] system because of some uncharged residues at its C-terminus {{PubMed\|16796683}}
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[sda]]'' {{PubMed\|11207367}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sda_2647456_2647614_1 sda] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|11207367}}
−
−	* '''Regulation:'''
−	** induced by DNA damage ([[LexA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16267290 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[DnaA]]: transcription activation under replication stress {{PubMed\|17932079}}
−	** [[LexA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16267290 PubMed]
−
−	* '''Additional information:'''
−	** Sda is rapidly turned over by the [[ClpP\|ClpP/X]] system because of some uncharged residues at its C-terminus {{PubMed\|16796683}}.
−	** An [[ncRNA\|antisense RNA]] is predicted for ''[[sda]]'' {{PubMed\|20525796}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** 1A1034 (no resistance), {{PubMed\|16796683}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A1034&Search=1A1034 BGSC]
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~[[Bill Burkholder]] [http://burkholder.stanford.edu/ Homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed> 22933559</pubmed>~~
−	~~== Original publications ==~~
−	~~<pubmed>11207367, 16267290, 19465772, 15023339 16796683 19684115 17932079 17350039 19101565 20525796 26020636</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 47: / Line 47: @@
 = This gene is a member of the following [[regulons]] =
 {{SubtiWiki regulon|[[LexA regulon]]}}
@@ Line 92: / Line 93: @@
 * '''[[SubtInteract|Interactions]]:'''
 ** [[KinB]]-[[Sda]] {{PubMed|19465772}}
-**  [[KinA]]-[[Sda]] {{PubMed|15023339}}
+** [[KinA]]-[[Sda]] {{PubMed|15023339}}
 * '''[[Localization]]:'''
@@ Line 108: / Line 109: @@
 === Additional information===
+* [[Sda]] is rapidly degraded by the [[ClpP|ClpP/X]] system because of some uncharged residues at its C-terminus {{PubMed|16796683}}
 =Expression and regulation=
@@ Line 123: / Line 123: @@
 * '''Regulatory mechanism:'''
-** probably activated by [[DnaA]] under replication stress {{PubMed|17932079}}
+** [[DnaA]]: transcription activation under replication stress {{PubMed|17932079}}
 ** [[LexA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16267290 PubMed]
@@ Line 155: / Line 155: @@
 <pubmed> 22933559</pubmed>
 == Original publications ==
-<pubmed>11207367, 16267290, 19465772, 15023339 16796683 19684115 17932079 17350039 19101565 20525796</pubmed>
+<pubmed>11207367, 16267290, 19465772, 15023339 16796683 19684115 17932079 17350039 19101565 20525796 26020636</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 60: / Line 60: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sda.html]
@@ Line 96: / Line 97: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=3D36 3D36] (from Geobacillus stearothermophilus, complex with [[KinB]]) {{PubMed|19101565}},  [http://www.rcsb.org/pdb/explore.do?structureId=1PV0 1PV0]

@@ Line 19: / Line 19: @@
 |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=Sda Sda]
 |-
-|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=sda sda]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 5.605

@@ Line 17: / Line 17: @@
 |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=BSU25690 sda]
 |-
-|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/Sda Sda]
+|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=Sda Sda]
 |-
 |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 40: / Line 40: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
@@ Line 120: / Line 115: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sda_2647456_2647614_1 sda] {{PubMed|22383849}}
-* '''Sigma factor:'''  [[SigA]] {{PubMed|11207367}}
+* '''[[Sigma factor]]:'''  [[SigA]] {{PubMed|11207367}}
 * '''Regulation:'''
@@ Line 155: / Line 150: @@
 =References=
+==Reviews==
 <pubmed>11207367, 16267290, 19465772, 15023339 16796683 19684115 17932079 17350039 19101565 20525796</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 32: / Line 32: @@
   <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=sda_2647456_2647614_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:sda_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sda_2647456_2647614_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:sda_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU25690]]
 |-
 |}

@@ Line 27: / Line 27: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yloV]]'', ''[[yqeF]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU25690 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU25690 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU25690 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU25690 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU25690 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU25690 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:sda_context.gif]]

← Older revision		Revision as of 10:45, 20 September 2012
Line 136:		Line 136:

	* '''Mutant:'''		* '''Mutant:'''
		+	** 1A1034 (no resistance), {{PubMed\|16796683}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A1034&Search=1A1034 BGSC]

	* '''Expression vector:'''		* '''Expression vector:'''