YmdB - Revision history

Jstuelk: /* References */

2015-04-30T15:04:44Z

‎References

134.76.70.252 at 09:49, 17 April 2014

2014-04-17T09:49:13Z

134.76.38.147 at 13:47, 2 April 2014

2014-04-02T13:47:04Z

JGerwig: /* Biological materials */

2014-01-27T17:03:33Z

‎Biological materials

Jstuelk at 17:39, 14 December 2013

2013-12-14T17:39:44Z

Jstuelk: /* Database entries */

2013-12-14T17:35:03Z

‎Database entries

Jstuelk at 17:21, 14 December 2013

2013-12-14T17:21:00Z

Jstuelk at 12:28, 29 October 2013

2013-10-29T12:28:42Z

Jstuelk: /* Database entries */

2013-07-31T19:00:12Z

‎Database entries

134.76.70.252 at 13:25, 16 May 2013

2013-05-16T13:25:37Z

← Older revision		Revision as of 15:04, 30 April 2015
Line 1:		Line 1:
−	* '''Description:~~''' phosphodiesterase, controls bistable gene expression <br/><br/>~~	+	{{#bank: YmdB}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''ymdB''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| phosphodiesterase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| control of bistable gene expression~~
−	\|-
−	\|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=BSU16970 ymdB]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 29,1 kDa, 6.50~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 792 bp, 264 amino acids~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[rny]]'', ''[[spoVS]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16970 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16970 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16970 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ymdB_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=ymdB_1768941_1769735_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ymdB_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16970]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[biofilm formation]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU16970
−
−	~~===Phenotypes of a mutant ===~~
−	* strong overexpression of ''[[hag]]'' {{PubMed\|21856853}}
−	* defective in [[biofilm formation]] {{PubMed\|21856853,22113911}}
−	* the phenotypes of the ''ymdB'' mutant can be suppressed by overexpression of ''[[slrR]]'' {{PubMed\|21856853}}
−	* inactivation of ''[[ymdB]]'' restores beta-lactam resistance in a ''[[sigM]]'' mutant {{PubMed\|22211522}}
−	* increased expression of genes encoding small acid-soluble proteins {{PubMed\|24163345}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16970&redirect=T BSU16970]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13421]
−
−	* '''GEO entry:''' [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39142 GSE39142] (''[[ymdB]] '' mutant vs. wild type) {{PubMed\|24163345}}
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** phosphodiesterase activity toward 2',3'-cAMP {{PubMed\|24163345}}
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** forms tetramers {{PubMed\|24163345}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16970&redirect=T BSU16970]
−
−	* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=4B2O 4B2O] {{PubMed\|24163345}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O31775 O31775]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16970]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[rny]]-[[ymdB]]'' (weak readthrough transcription) {{PubMed\|21856853}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ymdB_1768941_1769735_1 ymdB] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:''' constitutive
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:''' there is a terminator between ''rny'' and ''[[ymdB]]'', most transcripts terminate there {{PubMed\|21856853}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 57 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 237 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** GP583 (spc), available in [[Jörg Stülke]]'s lab {{PubMed\|21856853}}
−	** GP922 (cat), available in [[Jörg Stülke]]'s lab {{PubMed\|21856853}}
−	** GP921 (spc) NCIB3610 derivate, available in [[Jörg Stülke]]'s lab {{PubMed\|21856853}}
−	** GP969 (''[[ymdB]]''(E39Q)-cat) inactive enzyme, available in [[Jörg Stülke]]'s lab {{PubMed\|24163345}}
−	** GP1558 (aphA3; cassette w/o terminator), available in [[Jörg Stülke]]'s lab
−	** GP1573 (aphA3), available in [[Jörg Stülke]]'s lab
−
−	* '''Expression vector:'''
−	** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP1041, available in [[Jörg Stülke]]'s lab
−	** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], in [[pGP382]]: pGP1919, available in [[Jörg Stülke]]'s lab
−	** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP1040, available in [[Jörg Stülke]]'s lab
−	** for expression/ purification from ''E. coli'' with N-terminal Strep-tag, in [[pGP172]]: pGP1917, available in [[Jörg Stülke]]'s lab {{PubMed\|24163345}}
−	** GP970 (''[[ymdB]]''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Jörg Stülke]]'s lab
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
−
−	* '''FLAG-tag construct:''' GP1018 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~[[Stülke\|Jörg Stülke]], University of Göttingen, Germany~~
−	~~[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed>21856853 22211522,22113911 24163345 </pubmed>~~
−	~~==Functional and structural analysis of orthologs in other organisms==~~
−	~~<pubmed> 19376879 17847097 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

← Older revision		Revision as of 09:49, 17 April 2014
Line 121:		Line 121:

	* '''Additional information:''' there is a terminator between ''rny'' and ''[[ymdB]]'', most transcripts terminate there {{PubMed\|21856853}}		* '''Additional information:''' there is a terminator between ''rny'' and ''[[ymdB]]'', most transcripts terminate there {{PubMed\|21856853}}
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 57 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 237 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 57: / Line 57: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 95: / Line 96: @@
 === Database entries ===
 * '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=4B2O 4B2O] {{PubMed|24163345}}

@@ Line 127: / Line 127: @@
 ** GP921 (spc) NCIB3610 derivate, available in [[Jörg Stülke]]'s lab {{PubMed|21856853}}
 ** GP969 (''[[ymdB]]''(E39Q)-cat) inactive enzyme, available in [[Jörg Stülke]]'s lab {{PubMed|24163345}}
 * '''Expression vector:'''

@@ Line 54: / Line 54: @@
 * the phenotypes of the ''ymdB'' mutant can be suppressed by overexpression of ''[[slrR]]'' {{PubMed|21856853}}
 * inactivation of ''[[ymdB]]'' restores beta-lactam resistance in a ''[[sigM]]'' mutant {{PubMed|22211522}}
 === Database entries ===
@@ Line 61: / Line 62: @@
 * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13421]
-* '''GEO entry:''' [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39142 GSE39142] (''[[ymdB]] '' mutant vs. wild type)
+* '''GEO entry:''' [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39142 GSE39142] (''[[ymdB]] '' mutant vs. wild type) {{PubMed|24163345}}
 === Additional information===
@@ Line 89: / Line 90: @@
 * '''[[SubtInteract|Interactions]]:'''
 * '''[[Localization]]:'''

← Older revision		Revision as of 17:35, 14 December 2013
Line 60:		Line 60:

	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13421]		* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13421]
		+
		+	* '''GEO entry:''' [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39142 GSE39142] (''[[ymdB]] '' mutant vs. wild type)

	=== Additional information===		=== Additional information===

@@ Line 78: / Line 78: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 119: / Line 119: @@
 * '''Mutant:'''
-** GP583 (spc), available in [[Stülke]] lab
+** GP583 (spc), available in [[Jörg Stülke]]'s lab {{PubMed|21856853}}
-** GP922 (cat), available in [[Stülke]] lab
+** GP922 (cat), available in [[Jörg Stülke]]'s lab {{PubMed|21856853}}
-** GP921 (spc) NCIB3610 derivate, available in [[Stülke]] lab
+** GP921 (spc) NCIB3610 derivate, available in [[Jörg Stülke]]'s lab {{PubMed|21856853}}
-** GP969 (''[[ymdB]]''(E39Q)-cat) inactive enzyme, available in [[Stülke]] lab
+** GP969 (''[[ymdB]]''(E39Q)-cat) inactive enzyme, available in [[Jörg Stülke]]'s lab {{PubMed|24163345}}
 * '''Expression vector:'''
-** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP1041, available in [[Stülke]] lab
+** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP1041, available in [[Jörg Stülke]]'s lab
-** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], in [[pGP382]]: pGP1919, available in [[Stülke]] lab
+** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], in [[pGP382]]: pGP1919, available in [[Jörg Stülke]]'s lab
-** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP1040, available in [[Stülke]] lab
+** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP1040, available in [[Jörg Stülke]]'s lab
-** for expression/ purification from ''E. coli'' with N-terminal Strep-tag, in [[pGP172]]: pGP1917, available in [[Stülke]] lab
+** for expression/ purification from ''E. coli'' with N-terminal Strep-tag, in [[pGP172]]: pGP1917, available in [[Jörg Stülke]]'s lab {{PubMed|24163345}}
-** GP970 (''[[ymdB]]''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab
+** GP970 (''[[ymdB]]''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Jörg Stülke]]'s lab
 * '''lacZ fusion:'''
@@ Line 135: / Line 135: @@
 * '''GFP fusion:'''
-* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
-* '''FLAG-tag construct:''' GP1018 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab
+* '''FLAG-tag construct:''' GP1018 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab
 * '''Antibody:'''

@@ Line 67: / Line 67: @@
 === Basic information/ Evolution ===
-* '''Catalyzed reaction/ biological activity:''' phosphatase activity toward phosphoenolpyruvate and phosphodiesterase activity toward 2',3'-cAMP (the ''Deinococcus'' ortholog) {{PubMed|17847097}}
+* '''Catalyzed reaction/ biological activity:'''
 * '''Protein family:'''
@@ Line 91: / Line 92: @@
 === Database entries ===
-* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=4B2O 4B2O]
+* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=4B2O 4B2O] {{PubMed|24163345}}
 * '''UniProt:''' [http://www.uniprot.org/uniprot/O31775 O31775]
@@ Line 148: / Line 149: @@
 =References=
-<pubmed>21856853 22211522,22113911</pubmed>
+<pubmed>21856853 22211522,22113911 24163345 </pubmed>
 ==Functional and structural analysis of orthologs in other organisms==
 <pubmed> 19376879 17847097 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 27: / Line 27: @@
   <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=ymdB_1768941_1769735_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ymdB_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ymdB_1768941_1769735_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ymdB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16970]]
 |-
 |}