ClpX - Revision history

Jstuelk: /* Original Publications */

2015-06-11T09:12:19Z

‎Original Publications

Jstuelk: /* Original Publications */

2014-12-05T18:17:21Z

‎Original Publications

Jstuelk at 10:51, 20 June 2014

2014-06-20T10:51:54Z

134.76.70.252 at 09:47, 17 April 2014

2014-04-17T09:47:41Z

134.76.38.147 at 14:25, 2 April 2014

2014-04-02T14:25:24Z

Jstuelk at 09:32, 16 January 2014

2014-01-16T09:32:00Z

134.76.70.252 at 11:23, 7 January 2014

2014-01-07T11:23:02Z

134.76.70.252 at 09:03, 12 November 2013

2013-11-12T09:03:05Z

134.76.70.252 at 14:11, 16 May 2013

2013-05-16T14:11:20Z

134.76.70.252 at 10:55, 14 May 2013

2013-05-14T10:55:04Z

← Older revision		Revision as of 09:12, 11 June 2015
Line 1:		Line 1:
−	* '''Description:~~''' ATP-dependent Clp protease ATP-binding subunit (class III heat-shock protein) <br/><br/>~~	+	{{#bank: ClpX}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''clpX''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| ATP-dependent Clp protease ATP-binding subunit~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| protein degradation~~
−	\|-
−	\|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=BSU28220 clpX]
−	\|-
−	\|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=ClpX ClpX]
−	\|-
−	\|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=clpX clpX]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 46 kDa, 4.645~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1260 bp, 420 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[lonB]]'', ''[[tig]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28220 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28220 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28220 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:clpX_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=clpX_2884781_2886043_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:clpX_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU28220]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[proteolysis]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CtsR regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU28220
−
−	~~===Phenotypes of a mutant ===~~
−	* increased thermotolerance due to increased stabiliy of [[Spx]] and thus increased expression of ''[[trxA]]'' {{PubMed\|24417481}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU28220&redirect=T BSU28220]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/clpX.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11387]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' ATPase/chaperone
−
−	* '''Protein family:''' clpX chaperone family (according to Swiss-Prot) ClpX (IP004487) [http://www.ebi.ac.uk/interpro/IEntry?ac=IPR004487 InterPro], AAA+ -type ATPase (IPR013093) [http://www.ebi.ac.uk/interpro/IEntry?ac=IPR013093 InterPro] (PF07724) [http://pfam.sanger.ac.uk/family?acc=PF07724 PFAM]
−
−	* '''Paralogous protein(s):''' [[ClpC]], [[ClpE]]
−
−	~~=== Targets of [[ClpX]]-[[ClpP]]-dependent protein degradation ===~~
−	* [[MgsR]] {{PubMed\|22812682}}
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−	** AAA-ATPase [http://pfam.sanger.ac.uk/family?acc=PF07724 PFAM]
−	** Zinc finger [http://pfam.sanger.ac.uk/family?acc=PF06689 PFAM]
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[ClpP]]-[[ClpX]]
−	** [[Spx]]-[[ClpP]]/[[ClpX]] (degradation of [[Spx]]) {{PubMed\|17827297}}
−
−	* '''[[Localization]]:''' cytoplasmic polar clusters, excluded from the nucleoid, induced clustering upon heat shock, colocalization with [[ClpP]] {{PubMed\|18786145,18689473}}
−	~~[[File:ClpX.jpg‎ ]]~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU28220&redirect=T BSU28220]
−
−	* '''Structure:''' homologue structure resolved [http://www.rcsb.org/pdb/explore/explore.do?structureId=1UM8 1UM8], structural model of ''B. subtilis'' ClpX available from [http://subtiwiki.uni-goettingen.de/wiki/index.php/User:Hstrahl hstrahl]
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P50866 P50866]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU28220]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''clpX'' {{PubMed\|11325926}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=clpX_2884781_2886043_-1 clpX] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|8973311}}
−
−	* '''Regulation:'''
−	** induced by heat stress ([[CtsR]]) {{PubMed\|9852015}}
−
−	* '''Regulatory mechanism:'''
−	** [[CtsR]]: transcription repression {{PubMed\|9852015}}
−
−	* '''Additional information:'''
−	** The mRNA has a long 5' leader region. This may indicate RNA-based regulation {{PubMed\|20525796}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 1690 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 6358 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:''' ''clpX::kan'', ''clpX::spec'' and ''clpX::cat'' available from the [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:''' C-terminal GFP fusions (both single copy and 2th copy in ''amyE'' locus, also as CFP and YFP variants) available from the [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−	~~[[Leendert Hamoen]], Newcastle University, UK [http://www.ncl.ac.uk/camb/staff/profile/l.hamoen homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>23375660 19680248 17302811 23479438,19609260</pubmed>~~
−	~~==Original Publications==~~
−	~~<pubmed>12761164 10809708,9643546,11807061,14679237,18689476,16899079,8973311, 19136590 , 11325926 8973311 9852015 18689473 20525796 15948963 18786145 24417481 24942655 25433860 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 156: / Line 156: @@
 <pubmed>23375660  19680248 17302811 23479438,19609260</pubmed>
 ==Original Publications==
-<pubmed>12761164 10809708,9643546,11807061,14679237,18689476,16899079,8973311, 19136590 , 11325926 8973311 9852015 18689473 20525796 15948963 18786145 24417481 24942655 </pubmed>
+<pubmed>12761164 10809708,9643546,11807061,14679237,18689476,16899079,8973311, 19136590 , 11325926 8973311 9852015 18689473 20525796 15948963 18786145 24417481 24942655 25433860 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 156: / Line 156: @@
 <pubmed>23375660  19680248 17302811 23479438,19609260</pubmed>
 ==Original Publications==
-<pubmed>12761164 10809708,9643546,11807061,14679237,18689476,16899079,8973311, 19136590 , 11325926 8973311 9852015 18689473 20525796 15948963 18786145 24417481</pubmed>
+<pubmed>12761164 10809708,9643546,11807061,14679237,18689476,16899079,8973311, 19136590 , 11325926 8973311 9852015 18689473 20525796 15948963 18786145 24417481 24942655 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 130: / Line 130: @@
 * '''Additional information:'''
 ** The mRNA has a long 5' leader region. This may indicate RNA-based regulation {{PubMed|20525796}}
 =Biological materials =

@@ Line 59: / Line 59: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/clpX.html]
@@ Line 101: / Line 102: @@
 === Database entries ===
 * '''Structure:''' homologue structure resolved [http://www.rcsb.org/pdb/explore/explore.do?structureId=1UM8 1UM8], structural model of ''B. subtilis'' ClpX available from [http://subtiwiki.uni-goettingen.de/wiki/index.php/User:Hstrahl hstrahl]

@@ Line 56: / Line 56: @@
 ===Phenotypes of a mutant ===
 === Database entries ===
@@ Line 64: / Line 65: @@
 === Additional information===
 =The protein=
@@ Line 85: / Line 83: @@
 * '''Kinetic information:'''
-* '''Domains:''' AAA-ATPase [http://pfam.sanger.ac.uk/family?acc=PF07724 PFAM], Zinc finger [http://pfam.sanger.ac.uk/family?acc=PF06689 PFAM]
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 150: / Line 150: @@
 =References=
 ==Reviews==
-'''Additional reviews: ''' {{PubMed|23479438,19609260}}
+<pubmed>23375660  19680248 17302811 23479438,19609260</pubmed>
 ==Original Publications==
-'''Additional publications: ''' {{PubMed|18786145}}
+<pubmed>12761164 10809708,9643546,11807061,14679237,18689476,16899079,8973311, 19136590 , 11325926 8973311 9852015 18689473 20525796 15948963 18786145 24417481</pubmed>
 [[Category:Protein-coding genes]]

@@ 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=ClpX ClpX]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/phosphorelay.html Phosphorelay], [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress]'''
+|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=clpX clpX]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 4.645

@@ 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=BSU28220 clpX]
 |-
-|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/ClpX ClpX]
+|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=ClpX ClpX]
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/phosphorelay.html Phosphorelay], [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress]'''

@@ Line 33: / Line 33: @@
   <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=clpX_2884781_2886043_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:clpX_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=clpX_2884781_2886043_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:clpX_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU28220]]
 |-
 |}

@@ Line 26: / Line 26: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lonB]]'', ''[[tig]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28220 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28220 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28220 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28220 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28220 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28220 DNA_with_flanks]
 |-
 |-