LeuB - Revision history

Jstuelk: /* References */

2015-07-30T13:00:55Z

‎References

Jstuelk: /* References */

2015-07-30T09:17:38Z

‎References

Jstuelk: /* References */

2014-09-19T12:37:02Z

‎References

134.76.70.252 at 14:09, 17 April 2014

2014-04-17T14:09:25Z

134.76.70.252 at 09:23, 17 April 2014

2014-04-17T09:23:55Z

134.76.38.147 at 14:25, 2 April 2014

2014-04-02T14:25:43Z

Jstuelk at 14:44, 5 March 2014

2014-03-05T14:44:32Z

134.76.70.252 at 11:23, 7 January 2014

2014-01-07T11:23:14Z

Jstuelk at 12:25, 22 December 2013

2013-12-22T12:25:31Z

134.76.70.252 at 14:11, 16 May 2013

2013-05-16T14:11:38Z

← Older revision		Revision as of 13:00, 30 July 2015
Line 1:		Line 1:
−	* '''Description:~~''' 3-isopropylmalate dehydrogenase <br/><br/>~~	+	{{#bank: LeuB}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''leuB''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''leuC ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| 3-isopropylmalate dehydrogenase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| biosynthesis of leucine~~
−	\|-
−	\|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=BSU28270 leuB]
−	\|-
−	\|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=leuB leuB]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 39 kDa, 4.744~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1095 bp, 365 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[leuC]]'', ''[[leuA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28270 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28270 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28270 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:leuB_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=leuB_2891020_2892117_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:leuB_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU28270]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[biosynthesis/ acquisition of amino acids]]}},~~
−	~~{{SubtiWiki category\|[[phosphoproteins]]}},~~
−	~~[[most abundant proteins]]~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CcpA regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[CodY regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[T-box]]}},~~
−	~~{{SubtiWiki regulon\|[[TnrA regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU28270
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU28270&redirect=T BSU28270]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ilvBHC-leuABCD.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10675]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' (2R,3S)-3-isopropylmalate + NAD<sup>+</sup> = 4-methyl-2-oxopentanoate + CO<sub>2</sub> + NADH (according to Swiss-Prot)
−
−	* '''Protein family:''' LeuB type 1 subfamily (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−	** phosphorylated on Arg-4 {{PubMed\|22517742}}
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU28270&redirect=T BSU28270]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1XAD 1XAD] (Thermus thermophilus)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P05645 P05645]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU28270]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.85 1.1.1.85]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[ilvB]]-[[ilvH]]-[[ilvC]]-[[leuA]]-[[leuB]]-[[leuC]]-[[leuD]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/1577690 PubMed]
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=leuB_2891020_2892117_-1 leuB] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1577690 PubMed]
−
−	* '''Regulation:'''
−	** for a complete overview on the regulation of the ilv operon, see [http://www.ncbi.nlm.nih.gov/pubmed/20935095 Brinsmade ''et al''.]
−	** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
−	** expression is stimulated in the presence of glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/12193635 PubMed]
−	** repressed in the absence of good nitrogen sources (glutamine or ammonium) ([[TnrA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/15547269 PubMed]
−	** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[CcpA]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/12193635 PubMed]
−	** [[T-box]]: tRNA-controlled [[RNA switch]] that mediates termination/antitermination
−	** [[TnrA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/15547269 PubMed]
−	** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
−
−	* '''Additional information:'''
−	** belongs to the 100 [[most abundant proteins]] {{PubMed\|15378759}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 6438 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 942 {{PubMed\|24696501}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 5218 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 2316 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 1868 {{PubMed\|21395229}}
−
−	~~=Biological materials =~~
−	* '''Mutant:'''
−	** 1A618 ( ''leuB''::''erm''), {{PubMed\|3015878}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A618&Search=1A618 BGSC]
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>15060025,12193635,19258532,8289305,18641142,15547269,12618455,22517742,15547269,12618455,12107147, 20935095 25157083 24163341 25755103 15378759</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 158: / Line 158: @@
 =References=
-<pubmed>15060025,12193635,19258532,8289305,18641142,15547269,12618455,22517742,15547269,12618455,12107147, 20935095 25157083 24163341 15378759</pubmed>
+<pubmed>15060025,12193635,19258532,8289305,18641142,15547269,12618455,22517742,15547269,12618455,12107147, 20935095 25157083 24163341 25755103 15378759</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 158: / Line 158: @@
 =References=
-<pubmed>15060025,12193635,19258532,8289305,18641142,15547269,12618455,22517742,15547269,12618455,12107147, 20935095 24163341 15378759</pubmed>
+<pubmed>15060025,12193635,19258532,8289305,18641142,15547269,12618455,22517742,15547269,12618455,12107147, 20935095 25157083 24163341 15378759</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 134: / Line 134: @@
 ** number of protein molecules per cell (minimal medium with glucose and ammonium): 6438 {{PubMed|24696501}}
 ** number of protein molecules per cell (complex medium with amino acids, without glucose): 942 {{PubMed|24696501}}
 =Biological materials =
 * '''Mutant:'''
 ** 1A618 ( ''leuB''::''erm''), {{PubMed|3015878}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A618&Search=1A618 BGSC]

@@ Line 132: / Line 132: @@
 * '''Additional information:'''
 ** belongs to the 100 [[most abundant proteins]] {{PubMed|15378759}}
 =Biological materials =

@@ Line 61: / Line 61: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ilvBHC-leuABCD.html]
@@ Line 96: / Line 97: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1XAD 1XAD] (Thermus thermophilus)

@@ Line 43: / Line 43: @@
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[biosynthesis/ acquisition of amino acids]]}},
-{{SubtiWiki category|[[phosphoproteins]]}}
+{{SubtiWiki category|[[phosphoproteins]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 66: / Line 67: @@
 === Additional information===
 =The protein=
@@ Line 131: / Line 129: @@
 * '''Additional information:'''
 =Biological materials =
@@ Line 153: / Line 152: @@
 =References=
-<pubmed>15060025,12193635,19258532,8289305,18641142,15547269,12618455,22517742,15547269,12618455,12107147, 20935095 24163341</pubmed>
+<pubmed>15060025,12193635,19258532,8289305,18641142,15547269,12618455,22517742,15547269,12618455,12107147, 20935095 24163341 15378759</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=BSU28270 leuB]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/ile_val_leu.html Ile, Leu, Val], [http://subtiwiki.uni-goettingen.de/pathways/CoA_synthesis.html Coenzyme A]'''
+|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=leuB leuB]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 39 kDa, 4.744

@@ Line 39: / Line 39: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 88: / Line 84: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
 ** phosphorylated on Arg-4 {{PubMed|22517742}}
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 119: / Line 115: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=leuB_2891020_2892117_-1 leuB] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1577690 PubMed]
+* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1577690 PubMed]
-* '''Regulation:''' for a complete overview on the regulation of the ilv operon, see [http://www.ncbi.nlm.nih.gov/pubmed/20935095 Brinsmade ''et al''.]
+* '''Regulation:'''
 ** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
 ** expression is stimulated in the presence of glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/12193635 PubMed]
@@ Line 156: / Line 153: @@
 =References=
-<pubmed>15060025,12193635,19258532,8289305,18641142,15547269,12618455,22517742,15547269,12618455,12107147, 20935095</pubmed>
+<pubmed>15060025,12193635,19258532,8289305,18641142,15547269,12618455,22517742,15547269,12618455,12107147, 20935095 24163341</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 31: / Line 31: @@
   <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=leuB_2891020_2892117_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:leuB_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=leuB_2891020_2892117_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:leuB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU28270]]
 |-
 |}