MutTA - Revision history

134.76.70.252 at 10:00, 17 April 2014

2014-04-17T10:00:35Z

134.76.38.147 at 14:35, 2 April 2014

2014-04-02T14:35:00Z

134.76.70.252 at 14:22, 16 May 2013

2013-05-16T14:22:57Z

134.76.70.252 at 11:05, 14 May 2013

2013-05-14T11:05:11Z

134.76.70.252 at 13:40, 13 May 2013

2013-05-13T13:40:41Z

Jstuelk at 07:42, 25 April 2013

2013-04-25T07:42:59Z

134.76.70.252 at 15:13, 7 August 2012

2012-08-07T15:13:57Z

Jstuelk at 08:47, 6 June 2012

2012-06-06T08:47:43Z

Jstuelk: /* References */

2012-06-06T08:41:27Z

‎References

134.76.70.252 at 11:36, 20 April 2012

2012-04-20T11:36:44Z

← Older revision		Revision as of 10:00, 17 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' error prevention oxidized guanine system, confers protection against oxidative stress to vegetative cells, moreover the protein has RNA pyrophosphohydrolase activity <br/><br/>~~	+	{{#bank: MutTA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''mutTA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ytkD'', ''rppH''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| 8-oxo-dGTPase (antimutator), RNA pyrophosphohydrolase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| DNA repair, RNA 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=BSU30630 mutTA]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 18 kDa, 5.952~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 474 bp, 158 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ytlD]]'', ''[[ytkC]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU30630 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU30630 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU30630 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ytkD_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=ytkD_3134983_3135459_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:mutTA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU30630]]
−	\|-
−	\|}
−
−	~~__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]]}},~~
−	~~{{SubtiWiki category\|[[RNases]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[SigF regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU30630
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU30630&redirect=T BSU30630]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ytkD.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13869]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** removal of pyrophosphate from the 5' end of mRNAs to make the RNA accessible for degradation by [[RNases]] {{PubMed\|21925382}}
−	** RppH requires at least two unpaired nucleotides at the 5' end of its RNA substrates and prefers three or more. The second of these 5'-terminal nucleotides must be G, whereas a less strict preference for a purine is evident at the third position, and A is slightly favored over G at the first position {{PubMed\|23610425,23610407}}
−
−	* '''Protein family:''' [[Nudix hydrolase]] family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU30630&redirect=T BSU30630]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=4JZV 4JZV] {{PubMed\|23610407}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O35013 O35013]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU30630]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[mutTA]]'' {{PubMed\|9387221}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytkD_3134983_3135459_-1 mutTA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|14761999}}, [[SigF]] {{PubMed\|14761999}}
−
−	* '''Regulation:'''
−	** expressed during logarithmic growth ([[SigA]]) and early during sporulation in the forespore ([[SigF]]) {{PubMed\|16497325}}
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~== Reviews ==~~
−	~~<pubmed> 22568516</pubmed>~~
−	~~== Original publications ==~~
−	~~<pubmed>16513759,16497325, 14761999, 19011023 9387221 15576788 21925382 23610425 23610407 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 54: / Line 54: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ytkD.html]
@@ Line 93: / Line 94: @@
 === Database entries ===
 * '''Structure:'''	[http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=4JZV 4JZV] {{PubMed|23610407}}

@@ 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=ytkD_3134983_3135459_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:mutTA_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytkD_3134983_3135459_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:mutTA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU30630]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytlD]]'', ''[[ytkC]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU30630 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU30630 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU30630 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU30630 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU30630 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU30630 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ytkD_context.gif]]

@@ Line 14: / Line 14: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || DNA repair, RNA degradation
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU30630 mutTA]
+|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=BSU30630 mutTA]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 18 kDa, 5.952
@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytlD]]'', ''[[ytkC]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15041&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU30630 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU30630 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU30630 Advanced_DNA]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ytkD_context.gif]]

@@ Line 35: / Line 35: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
@@ Line 74: / Line 70: @@
 * '''Catalyzed reaction/ biological activity:'''
 ** removal of pyrophosphate from the 5' end of mRNAs to make the RNA accessible for degradation by [[RNases]] {{PubMed|21925382}}
 * '''Protein family:''' [[Nudix hydrolase]] family (according to Swiss-Prot)
@@ Line 97: / Line 94: @@
 === Database entries ===
-* '''Structure:'''
+* '''Structure:'''	[http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=4JZV 4JZV] {{PubMed|23610407}}
 * '''UniProt:''' [http://www.uniprot.org/uniprot/O35013 O35013]
@@ Line 113: / Line 110: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytkD_3134983_3135459_-1 mutTA] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] {{PubMed|14761999}}, [[SigF]] {{PubMed|14761999}}
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|14761999}}, [[SigF]] {{PubMed|14761999}}
 * '''Regulation:'''
@@ Line 142: / Line 139: @@
 =References=
 == Reviews ==
- <big>''Lehnik-Habrink M, Lewis RJ, Mäder U, Stülke J''  </big>
+<pubmed> 22568516</pubmed>
 == Original publications ==
-<pubmed>16513759,16497325, 14761999, 19011023 9387221 15576788 21925382 </pubmed>
+<pubmed>16513759,16497325, 14761999, 19011023 9387221 15576788 21925382 23610425 23610407 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 41: / Line 41: @@
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[DNA repair/ recombination]]}},
-{{SubtiWiki category|[[sporulation proteins]]}}
+{{SubtiWiki category|[[sporulation proteins]]}},
 = This gene is a member of the following [[regulons]] =