GuaB - Revision history

Jstuelk: /* References */

2015-02-28T18:18:38Z

‎References

Jstuelk: /* References */

2015-02-10T17:59:13Z

‎References

134.76.70.252 at 14:08, 17 April 2014

2014-04-17T14:08:01Z

134.76.70.252 at 09:53, 17 April 2014

2014-04-17T09:53:31Z

134.76.38.147 at 12:44, 2 April 2014

2014-04-02T12:44:52Z

Jstuelk at 16:01, 5 March 2014

2014-03-05T16:01:18Z

Jstuelk: /* Phenotypes of a mutant */

2014-02-06T16:41:40Z

‎Phenotypes of a mutant

134.76.70.252 at 09:56, 7 January 2014

2014-01-07T09:56:50Z

Jstuelk at 11:55, 22 December 2013

2013-12-22T11:55:48Z

Jstuelk at 11:53, 22 December 2013

2013-12-22T11:53:24Z

← Older revision		Revision as of 18:18, 28 February 2015
Line 1:		Line 1:
−	* '''Description:''' IMP dehydrogenase <br/><br/>	+	{{#bank: GuaB}}
−	{~~\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''guaB''~~
−	\|-
−	~~\|style="background:~~#~~ABCDEF;" align="center"\| '''Synonyms''' \|\| ''guaA ''~~
−	\|-
−	~~\|style="background~~:~~#ABCDEF;" align="center"\| '''Essential''' \|\| yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| IMP dehydrogenase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| biosynthesis of GMP~~
−	\|-
−	\|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=BSU00090 GuaB]
−	\|-
−	\|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=guaB guaB]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 52 kDa, 6.168~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1464 bp, 488 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yaaC]]'', ''[[dacA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00090 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00090 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00090 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:guaB_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=guaB_15915_17381_1 Expression at a glance]'''   {{PubMed\|22383849~~}~~}<br/>[[Image:guaB_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00090]]~~
−	\|-
−	\|}

−	~~__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 nucleotides]]}},~~
−	~~{{SubtiWiki category\|[[essential genes]]}},~~
−	~~{{SubtiWiki category\|[[phosphoproteins]]}},~~
−	~~[[most abundant proteins]]~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CodY regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU00090
−
−	~~===Phenotypes of a mutant ===~~
−	* essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
−	* reduced expression of ''[[guaB]]'' suppresses the requirement of a ''[[relA]] [[sasA]] [[sasB]]'' triple mutant for branched chain amino acids, methionine and threonine {{PubMed\|24163341}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00090&redirect=T BSU00090]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/guaB.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10073]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' Inosine 5'-phosphate + NAD<sup>+</sup> + H<sub>2</sub>O = xanthosine 5'-phosphate + NADH (according to Swiss-Prot)
−
−	* '''Protein family:''' IMPDH/GMPR family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−	** phosphorylated (STY) [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
−	** Cys308 is S-cysteinylated after diamide stress [http://www.ncbi.nlm.nih.gov/pubmed/17611193 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
−	** Cys308 is S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species [http://www.ncbi.nlm.nih.gov/pubmed/22938038 PubMed]
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−	** inhibition of enzymatic activity by (p)ppGpp during the ´stringent response´{{PubMed\|22981860,6111556}}
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00090&redirect=T BSU00090]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1VRD 1VRD] (from ''Thermotoga maritima msb8'', 60% identity, 80% similarity)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P21879 P21879]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00090]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.205 1.1.1.205]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''guaB'' {{PubMed\|22383849}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=guaB_15915_17381_1 guaB] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−	** activated during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[CodY]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
−
−	* '''Additional information:'''
−	** the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
−	** inhibition of enzymatic activity by (p)ppGpp during the ´stringent response´{{PubMed\|6111556}}
−	** belongs to the 100 [[most abundant proteins]] {{PubMed\|15378759}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 3210 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 20338 {{PubMed\|24696501}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 6450 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 4621 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 5993 {{PubMed\|21395229}}
−
−	~~=Biological materials =~~
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−	** purification from ''B. subtilis'' with an N-terminal Strep-tag, for [[SPINE]], (in [[pGP380]]): pGP901, available in [[Stülke]] lab
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed>22938038,17611193,12884008,1722815, 22981860,12618455,17726680 17726680 6111556 24163341 15378759 24682323</pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

@@ Line 152: / Line 152: @@
 =References=
-<pubmed>22938038,17611193,12884008,1722815, 22981860,12618455,17726680 17726680 6111556 24163341 15378759</pubmed>
+<pubmed>22938038,17611193,12884008,1722815, 22981860,12618455,17726680 17726680 6111556 24163341 15378759 24682323</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 129: / Line 129: @@
 ** number of protein molecules per cell (minimal medium with glucose and ammonium): 3210 {{PubMed|24696501}}
 ** number of protein molecules per cell (complex medium with amino acids, without glucose): 20338 {{PubMed|24696501}}
 =Biological materials =
 * '''Mutant:'''

@@ Line 127: / Line 127: @@
 ** inhibition of enzymatic activity by (p)ppGpp during the ´stringent response´{{PubMed|6111556}}
 ** belongs to the 100 [[most abundant proteins]] {{PubMed|15378759}}
 =Biological materials =

@@ Line 58: / Line 58: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/guaB.html]
@@ Line 96: / Line 97: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1VRD 1VRD] (from ''Thermotoga maritima msb8'', 60% identity, 80% similarity)

@@ Line 41: / Line 41: @@
 {{SubtiWiki category|[[biosynthesis/ acquisition of nucleotides]]}},
 {{SubtiWiki category|[[essential genes]]}},
-{{SubtiWiki category|[[phosphoproteins]]}}
+{{SubtiWiki category|[[phosphoproteins]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 63: / Line 64: @@
 === Additional information===
 =The protein=
@@ Line 124: / Line 124: @@
 ** the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
 ** inhibition of enzymatic activity by (p)ppGpp during the ´stringent response´{{PubMed|6111556}}
 =Biological materials =
@@ Line 145: / Line 146: @@
 =References=
-<pubmed>22938038,17611193,12884008,1722815, 22981860,12618455,17726680 17726680 6111556 24163341</pubmed>
+<pubmed>22938038,17611193,12884008,1722815, 22981860,12618455,17726680 17726680 6111556 24163341 15378759</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 54: / Line 54: @@
 ===Phenotypes of a mutant ===
 * essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
-* reduced expression of ''[[guaB]]''  suppresses the requirement of a ''[[relA]] [[yjbM]] [[ywaC]]'' triple mutant for branched chain amino acids, methionine and threonine {{PubMed|24163341}}
+* reduced expression of ''[[guaB]]''  suppresses the requirement of a ''[[relA]] [[sasA]] [[sasB]]'' triple mutant for branched chain amino acids, methionine and threonine {{PubMed|24163341}}
 === Database entries ===

@@ Line 15: / Line 15: @@
 |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=BSU00090 GuaB]
 |-
-|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/purine_biosynthesis.html Purine synthesis], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)]'''
+|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=guaB guaB]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 6.168

@@ Line 79: / Line 79: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
@@ Line 86: / Line 86: @@
 ** Cys308 is S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species [http://www.ncbi.nlm.nih.gov/pubmed/22938038 PubMed]
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 113: / Line 113: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=guaB_15915_17381_1 guaB] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:'''
@@ Line 145: / Line 145: @@
 =References=
+<pubmed>22938038,17611193,12884008,1722815, 22981860,12618455,17726680 17726680 6111556 24163341</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 36: / Line 36: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 53: / Line 53: @@
 ===Phenotypes of a mutant ===
+* essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
-essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+* reduced expression of ''[[guaB]]''  suppresses the requirement of a ''[[relA]] [[yjbM]] [[ywaC]]'' triple mutant for branched chain amino acids, methionine and threonine {{PubMed|24163341}}
 === Database entries ===