LigD - Revision history

Jstuelk: /* References */

2014-10-31T12:21:09Z

‎References

Jstuelk at 16:31, 20 December 2013

2013-12-20T16:31:51Z

Jstuelk at 16:30, 20 December 2013

2013-12-20T16:30:06Z

Jstuelk: /* Original publications */

2013-10-21T14:24:01Z

‎Original publications

Jstuelk: /* Reviews */

2013-09-13T17:05:06Z

‎Reviews

Jstuelk: /* Biological materials */

2013-08-08T15:52:53Z

‎Biological materials

Fabian Commichau: /* Biological materials */

2013-08-06T12:39:27Z

‎Biological materials

Fabian Commichau: /* Biological materials */

2013-08-06T12:37:12Z

‎Biological materials

Jstuelk: /* Extended information on the protein */

2013-05-23T11:36:15Z

‎Extended information on the protein

Jstuelk at 11:34, 23 May 2013

2013-05-23T11:34:40Z

← Older revision		Revision as of 12:21, 31 October 2014
Line 1:		Line 1:
−	* '''Description:~~''' DNA repair polymerase/ ligase in non-homologous end joining DNA repair <br/><br/>~~	+	{{#bank: LigD}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''ligD''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ykoU''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| DNA repair polymerase/ ligase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| non-homologous end joining DNA repair, repair of gapped DNA substrates~~
−	\|-
−	\|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=BSU13400 ligD]
−	\|-
−	\|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/LigD LigD]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 70 kDa, 6.646~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1833 bp, 611 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ykoT]]'', ''[[ykoV]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU13400 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU13400 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU13400 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ykoU_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=ykoU_1404518_1406353_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ykoU_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU13400]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[DNA repair/ recombination]]}},~~
−	~~{{SubtiWiki category\|[[sporulation proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[SigG regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SpoVT regulon]]}}~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU13400
−
−	~~===Phenotypes of a mutant ===~~
−	* sensitivity to ionizing radiation in the stationary phase {{PubMed\|12215643}}
−	* sensitivity of spores to several DNA-damaging treatments known to cause double strand breaks, such as UV-ray, X-ray, ultrahigh vacuum and wet heat {{PubMed\|16497325,17293412}}
−	* a ''[[ykoV]]-[[ligD]]'' double mutant is sensitive to radiation {{PubMed\|24123749}}
−
−	~~=== Database entries ===~~
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13264]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−	** N-terminal DNA ligase catalytic domain (aa 1 - 331) linked to a C-terminal polymerase domain (aa 332 - 611) {{PubMed\|23691176}}
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[YkoV]]-[[LigD]] {{PubMed\|23691176}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O34398 O34398]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13400]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[ykoV]]-[[ligD]]'' {{PubMed\|16497325}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ykoU_1404518_1406353_-1 ligD] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigG]] {{PubMed\|16497325}}
−
−	* '''Regulation:'''
−	** expressed during [[sporulation]] in the forespore ([[SigG]], [[SpoVT]]) {{PubMed\|16497325}}
−
−	* '''Regulatory mechanism:'''
−	** [[SpoVT]]: transcription activation {{PubMed\|16497325}}
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** BP141 (''[[ykoV]]-[[ligD]]''::''kan'') available in [[Fabian Commichau]]'s lab
−	** BP142 (''[[ykoW]]-[[ykoV]]-[[ligD]]''::''kan'') available in [[Fabian Commichau]]'s lab
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~== Reviews ==~~
−	~~<pubmed> 17938628 22933559 </pubmed>~~
−
−	~~== Original publications ==~~
−	~~<pubmed>16497325, 23691176, 12215643 11075926 11566200 17293412 24123749 24123749</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 57: / Line 57: @@
 * sensitivity to ionizing radiation in the stationary phase  {{PubMed|12215643}}
 * sensitivity of spores to several DNA-damaging treatments known to cause double strand breaks, such as UV-ray, X-ray, ultrahigh vacuum and wet heat {{PubMed|16497325,17293412}}
-* a ''[[ligD]]-[[ykoV]]'' double mutant is sensitive to radiation {{PubMed|24123749}}
+* a ''[[ykoV]]-[[ligD]]'' double mutant is sensitive to radiation {{PubMed|24123749}}
 === Database entries ===

@@ Line 57: / Line 57: @@
 * sensitivity to ionizing radiation in the stationary phase  {{PubMed|12215643}}
 * sensitivity of spores to several DNA-damaging treatments known to cause double strand breaks, such as UV-ray, X-ray, ultrahigh vacuum and wet heat {{PubMed|16497325,17293412}}
 === Database entries ===
@@ Line 64: / Line 66: @@
 === Additional information===
@@ Line 82: / Line 82: @@
 * '''Kinetic information:'''
-* '''Domains:'''  N-terminal DNA ligase catalytic domain (aa 1 - 331) linked to a C-terminal polymerase domain (aa 332 - 611) {{PubMed|23691176}}
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 148: / Line 149: @@
 == Original publications ==
-<pubmed>16497325, 23691176, 12215643 11075926 11566200 17293412 24123749 </pubmed>
+<pubmed>16497325, 23691176, 12215643 11075926 11566200 17293412 24123749 24123749</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 148: / Line 148: @@
 == Original publications ==
-<pubmed>16497325, 23691176, 12215643 11075926 11566200 17293412 </pubmed>
+<pubmed>16497325, 23691176, 12215643 11075926 11566200 17293412 24123749 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 145: / Line 145: @@
 =References=
 == Reviews ==
-<pubmed> 17938628 </pubmed>
+<pubmed> 17938628  22933559 </pubmed>
 == Original publications ==
 <pubmed>16497325, 23691176, 12215643 11075926 11566200 17293412 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 126: / Line 126: @@
 * '''Mutant:'''
-** BP141 (''[[ykoVU]]''::''kan'') available in [[Fabian Commichau]]'s lab
+** BP141 (''[[ykoV]]-[[ligD]]''::''kan'') available in [[Fabian Commichau]]'s lab
-** BP142 (''[[ykoWVU]]''::''kan'') available in [[Fabian Commichau]]'s lab
+** BP142 (''[[ykoW]]-[[ykoV]]-[[ligD]]''::''kan'') available in [[Fabian Commichau]]'s lab
 * '''Expression vector:'''

@@ Line 12: / Line 12: @@
 |style="background:#ABCDEF;" align="center"| '''Product''' || DNA repair polymerase/ ligase
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || non-homologous end joining DNA repair
+|style="background:#ABCDEF;" align="center"|'''Function''' || non-homologous end joining DNA repair, repair of gapped DNA substrates
 |-
 |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=BSU13400 ligD]