PgpH - Revision history

Jstuelk at 13:04, 5 August 2015

2015-08-05T13:04:26Z

Jstuelk: /* Original publications */

2015-08-05T12:58:31Z

‎Original publications

Jstuelk at 13:45, 8 May 2015

2015-05-08T13:45:44Z

Jstuelk: Jstuelk moved page YqfF to PgpH

2015-05-08T13:44:52Z

Jstuelk moved page YqfF to PgpH

Jstuelk: /* References */

2015-04-17T15:54:03Z

‎References

Jstuelk at 16:53, 1 April 2015

2015-04-01T16:53:00Z

Jgundlach: /* Biological materials */

2015-04-01T12:20:22Z

‎Biological materials

Jgundlach: /* Biological materials */

2015-04-01T12:18:35Z

‎Biological materials

Jstuelk: /* Database entries */

2015-02-25T11:34:40Z

‎Database entries

Jstuelk at 11:34, 25 February 2015

2015-02-25T11:34:03Z

← Older revision		Revision as of 13:04, 5 August 2015
Line 1:		Line 1:
−	* '''Description:~~''' c-di-AMP specific phosphodiesterase <br/><br/>~~	+	{{#bank: PgpH}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''pgpH''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yqfF ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| c-di-AMP specific phosphodiesterase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| control of c-di-AMP 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=BSU25330 pgpH]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 78 kDa, 7.697~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 2133 bp, 711 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yqfG]]'', ''[[phoH]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU25330 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU25330 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU25330 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yqfF_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=yqfF_2612282_2614417_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:yqfF_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU25330]]
−	\|-
−	\|}
−
−	~~__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:''' BSU25330
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU25330&redirect=T BSU25330]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11655]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** hydrolysis of c-di-AMP to 5'-pApA {{PubMed\|25583510}}
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''Cofactors:''' Mn(2+) {{PubMed\|25583510}}
−
−	* '''Effectors of protein activity:'''
−	** ppGpp acts as allosteric inhibitor of phosphodiesterase activity (in ''Listeria monocytogenes'') {{PubMed\|25583510}}
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[PgpH]] is a member of a suspected group of hubs proteins that were suggested to be involved in a large number of [[SubtInteract\|interactions]] {{PubMed\|21630458}}
−
−	* '''[[Localization]]:'''
−	** cell membrane {{PubMed\|25583510}} (according to UniProt)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU25330&redirect=T BSU25330]
−
−	* '''Structure:'''
−	** [http://pdb.org/pdb/explore/explore.do?structureId=4S1B 4S1B] (the HD domain of the protein from ''Listeria monocytogenes'' in complex with c-di-AMP, 58% identity, 85% similarity) {{PubMed\|25583510}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P46344 P46344]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25330]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:'''
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yqfF_2612282_2614417_-1 pgpH] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** SM-GN1 (''yqfF-spc''), available in [[Anne Galinier]]'s and [[Boris Görke]]'s labs
−	** BKE25330 (''[[yqfF]]''::''erm'' without terminator, available in the BGSC and in [[Jörg Stülke]]'s lab)
−	** GP2033 (''[[yqfF]]''::''tet'', available in [[Jörg Stülke]]'s lab)
−	** GP2034 (''[[yqfF]]''::''erm'' without terminator, available in [[Jörg Stülke]]'s lab)
−	** GP2049 (''[[yqfF]]''::''cat'' without terminator, available in [[Jörg Stülke]]'s lab)
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:''' pGP190 (in [[pAC7]]), available in [[Stülke]] lab
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>25637595 25869574 </pubmed>~~
−	~~==Original publications==~~
−	~~<pubmed>21630458 25583510 26240071 </pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

@@ Line 146: / Line 146: @@
 <pubmed>25637595 25869574 </pubmed>
 ==Original publications==
-<pubmed>21630458 25583510 </pubmed>
+<pubmed>21630458 25583510 26240071 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 4: / Line 4: @@
 |-
 |style="background:#ABCDEF;" align="center"|'''Gene name'''
-|''yqfF''
+|''pgpH''
 |-
-|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqfF ''
 |-
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no
@@ Line 14: / Line 14: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || control of c-di-AMP 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=BSU25330 yqfF]
+|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=BSU25330 pgpH]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 78 kDa, 7.697
@@ Line 86: / Line 86: @@
 * '''[[SubtInteract|Interactions]]:'''
-** [[YqfF]] is a member of a suspected group of hubs proteins that were suggested to be involved in a large number of [[SubtInteract|interactions]] {{PubMed|21630458}}
+** [[PgpH]] is a member of a suspected group of hubs proteins that were suggested to be involved in a large number of [[SubtInteract|interactions]] {{PubMed|21630458}}
 * '''[[Localization]]:'''
@@ Line 109: / Line 109: @@
 * '''Operon:'''
-* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yqfF_2612282_2614417_-1 yqfF] {{PubMed|22383849}}
+* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yqfF_2612282_2614417_-1 pgpH] {{PubMed|22383849}}
 * '''[[Sigma factor]]:'''

@@ Line 144: / Line 144: @@
 =References=
 ==Reviews==
-<pubmed>25637595</pubmed>
+<pubmed>25637595 25869574 </pubmed>
 ==Original publications==
 <pubmed>21630458 25583510 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 38: / Line 38: @@
 = [[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 88: / Line 89: @@
 * '''[[Localization]]:'''
 === Database entries ===

← Older revision	Revision as of 13:44, 8 May 2015
(No difference)

@@ Line 122: / Line 122: @@
 ** SM-GN1 (''yqfF-spc''), available in [[Anne Galinier]]'s and [[Boris Görke]]'s labs
 ** BKE25330 (''[[yqfF]]''::''erm'' without terminator, available in the BGSC and in [[Jörg Stülke]]'s lab)
 * '''Expression vector:'''

@@ Line 93: / Line 93: @@
 * '''Structure:'''
-** [http://pdb.org/pdb/explore/explore.do?structureId=4S1B 4S1B] (the HD domain of the protein from ''Listeria monocytogenes'' in complex with c-di-AMP) {{PubMed|25583510}}
+** [http://pdb.org/pdb/explore/explore.do?structureId=4S1B 4S1B] (the HD domain of the protein from ''Listeria monocytogenes'' in complex with c-di-AMP, 58% identity, 85% similarity) {{PubMed|25583510}}
 * '''UniProt:''' [http://www.uniprot.org/uniprot/P46344 P46344]

@@ Line 75: / Line 75: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''Cofactors:''' Mn(2+) {{PubMed|25583510}}
 * '''Effectors of protein activity:'''
 * '''[[SubtInteract|Interactions]]:'''
@@ Line 92: / Line 93: @@
 * '''Structure:'''
 * '''UniProt:''' [http://www.uniprot.org/uniprot/P46344 P46344]