GdpP - Revision history

Jstuelk: /* Original publications */

2015-08-05T13:00:13Z

‎Original publications

Jstuelk: /* References */

2015-04-17T15:52:43Z

‎References

Jstuelk: /* Extended information on the protein */

2015-02-25T14:36:32Z

‎Extended information on the protein

Jstuelk at 14:34, 25 February 2015

2015-02-25T14:34:38Z

Jstuelk: /* References */

2015-01-28T09:43:07Z

‎References

134.76.70.252 at 11:39, 8 April 2014

2014-04-08T11:39:20Z

134.76.38.147 at 15:17, 2 April 2014

2014-04-02T15:17:16Z

134.76.70.252 at 15:02, 16 May 2013

2013-05-16T15:02:17Z

134.76.70.252 at 11:44, 14 May 2013

2013-05-14T11:44:58Z

134.76.70.252 at 14:19, 13 May 2013

2013-05-13T14:19:51Z

← Older revision		Revision as of 13:00, 5 August 2015
Line 1:		Line 1:
−	* '''Description:~~''' cyclic di-AMP phosphodiesterase~~	+	{{#bank: GdpP}}
−	~~<br/><br/>~~

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''gdpP''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yybT ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| c-di-AMP phosphodiesterase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| control of sporulation initiation, cell wall homeostasis~~
−	\|-
−	\|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=BSU40510 gdpP]
−	\|-
−	\|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=GdpP GdpP]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 74 kDa, 4.865~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1977 bp, 659 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[rplI]]'', ''[[yybS]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40510 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40510 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40510 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yybT_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=yybT_4163643_4165622_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:gdpP_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU40510]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[metabolism of signalling nucleotides]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}}~~
−
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU40510
−
−	~~===Phenotypes of a mutant ===~~
−	* inactivation of ''[[gdpP]]'' strongly restores beta-lactam resistance in a ''[[sigM]]'' mutant {{PubMed\|22211522}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU40510&redirect=T BSU40510]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yybST-rplI.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10010]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** cyclic dinucleotide phosphodiesterase, hydrolysis of di-cyclic AMP {{PubMed\|19901023}}
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−	** two transmembrane domains at the N-terminus {{PubMed\|19901023}}
−	** a domain that shares minimum sequence homology with Heme-binding [[PAS domain\|Per-ARNT-Sim (PAS) domains]] (80 aa) {{PubMed\|21257773}}
−	** degenerate GGDEF domain (aa 173 - 301) {{PubMed\|19901023}}
−	** DHH/ DHHA1 phosphodiesterase domain {{PubMed\|19901023}}
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−	** ppGpp inhibits cyclic dinucleotide phosphodiesterase activity {{PubMed\|19901023}}
−	** Heme binding suppresses phosphodiesterase activity {{PubMed\|21257773}}
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU40510&redirect=T BSU40510]
−
−	* '''Structure:'''
−	** [http://www.rcsb.org/pdb/explore/explore.do?structureId=2M1C 2M1C] (N-terminal PAS domain of GdpP from ''Geobacillus thermodenitrificans'') {{PubMed\|23504327}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P37484 P37484]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40510]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[yybS]]-[[gdpP]]-[[rplI]]'' (according to [http://dbtbs.hgc.jp/COG/prom/yybST-rplI.html DBTBS])
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yybT_4163643_4165622_-1 gdpP] {{PubMed\|22383849}}
−
−	* '''Sigma factor:'''
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−	** there is an internal [[SigD]]-dependent antisense transcript (as-''[[gdpP]]'') {{PubMed\|22956758}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** GP998 (''[[gdpP]]''::''spc''), available in [[Jörg Stülke]]'s lab
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed> 25869574</pubmed>~~
−	~~==Original publications==~~
−	~~<pubmed> 19901023 21257773 21566650 23504327 22211522,22956758 25616256</pubmed>~~
−	~~==GdpP homologs in other organisms==~~
−	~~<pubmed> 18502872 </pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

@@ Line 148: / Line 148: @@
 =References=
 <pubmed> 19901023 21257773 21566650 23504327 22211522,22956758 25616256</pubmed>
 ==GdpP homologs in other organisms==
 <pubmed> 18502872  </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 82: / Line 82: @@
 * '''[[Domains]]:'''
-** two transmembrane domains at the N-terminus
+** two transmembrane domains at the N-terminus {{PubMed|19901023}}
 ** a domain that shares minimum sequence homology with Heme-binding [[PAS domain|Per-ARNT-Sim (PAS) domains]] (80 aa) {{PubMed|21257773}}
-** degenerate GGDEF domain (aa 173 - 301) {{PubMed|22211522}}
+** degenerate GGDEF domain (aa 173 - 301) {{PubMed|19901023}}
-** DHH/ DHHA1 phosphodiesterase domain {{PubMed|22211522}}
+** DHH/ DHHA1 phosphodiesterase domain {{PubMed|19901023}}
 * '''Modification:'''
-* '''Cofactor(s):''' b-type heme with 1:1 stoichiometry {{PubMed|21257773}}
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''

@@ Line 41: / Line 41: @@
 = [[Categories]] containing this gene/protein =
-{{SubtiWiki category|[[metabolism of signalling nucleotides]]}}
+{{SubtiWiki category|[[metabolism of signalling nucleotides]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 54: / Line 56: @@
 ===Phenotypes of a mutant ===
 * inactivation of ''[[gdpP]]'' strongly restores beta-lactam resistance in a ''[[sigM]]'' mutant {{PubMed|22211522}}
 === Database entries ===
 * '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU40510&redirect=T BSU40510]
@@ Line 78: / Line 81: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
-** N-terminal domain that shares minimum sequence homology with Haem-binding Per-ARNT-Sim (PAS) domains (80 aa) {{PubMed|21257773}}
+** two transmembrane domains at the N-terminus
 ** degenerate GGDEF domain (aa 173 - 301) {{PubMed|22211522}}
 ** DHH/ DHHA1 phosphodiesterase domain {{PubMed|22211522}}

@@ Line 144: / Line 144: @@
 =References=
-<pubmed> 19901023 21257773 21566650 23504327 22211522,22956758</pubmed>
+<pubmed> 19901023 21257773 21566650 23504327 22211522,22956758 25616256</pubmed>
 ==GdpP homologs in other organisms==
 <pubmed> 18502872  </pubmed>
 [[Category:Protein-coding genes]]

@@ 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=BSU40510 gdpP]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 74 kDa, 4.865

@@ Line 53: / Line 53: @@
 * inactivation of ''[[gdpP]]'' strongly restores beta-lactam resistance in a ''[[sigM]]'' mutant {{PubMed|22211522}}
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yybST-rplI.html]
@@ Line 93: / Line 94: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 28: / Line 28: @@
   <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=yybT_4163643_4165622_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:gdpP_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yybT_4163643_4165622_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:gdpP_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU40510]]
 |-
 |}

@@ Line 23: / Line 23: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rplI]]'', ''[[yybS]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40510 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40510 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40510 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40510 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40510 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40510 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yybT_context.gif]]