Difference between revisions of "Sandbox"

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−
* '''Description:''' protein arginine kinase, phosphorylates [[CtsR]], modulator of [[CtsR]]-dependent repression <br/><br/>
+
* '''Description:''' formation of 2-deoxy-5-keto-gluconic acid (4th reaction) <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''mcsB''
+
|''iolB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yacI ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxdB ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || protein arginine kinase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || formation of 2-deoxy-5-keto-gluconic acid (4th reaction)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[CtsR]] activity
+
|style="background:#ABCDEF;" align="center"|'''Function''' || myo-inositol catabolism
 
|-
 
|-
−
|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/stress_response.html Stress]'''
+
|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/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 5.068  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 4.77  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1089 bp, 363 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 813 bp, 271 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mcsA]]'', ''[[clpC]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[iolC]]'', ''[[iolA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11861&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16011&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:mcsB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:iolB_context.gif]]
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00850
+
* '''Locus tag:''' BSU39750
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ctsR-mcsAB-clpC-radA-yacK.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/mmsA-iolBCDEF-idh-iolHI-fbaB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10147]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11118]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' phosphorylation of [[CtsR]] on Arg-62 [http://www.ncbi.nlm.nih.gov/sites/entrez/19498169 PubMed]
+
* '''Catalyzed reaction/ biological activity:''' 5-deoxy-glucuronic acid = 5-dehydro-2-deoxy-D-gluconic acid (according to Swiss-Prot)
  
−
* '''Protein family:''' ATP:guanido phosphotransferase family (according to Swiss-Prot)
+
* '''Protein family:''' isomerase iolB family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[McsA]]-[[McsB]]-[[CtsR]],  [[McsB]]-[[CtsR]],  [[McsB]]-[[ClpC]],  [[McsA]]-[[McsB]]
+
* '''Interactions:'''
  
 
* '''Localization:'''
 
* '''Localization:'''
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P42413 P42413]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00850]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU39750]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 90: Line 90:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[ctsR]]-[[mcsA]]-[[mcsB]]-[[clpC]]-[[radA]]-[[disA]]'' [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed]
+
* '''Operon:''' ''[[iolA]]-[[iolB]]-[[iolC]]-[[iolD]]-[[iolE]]-[[iolF]]-[[iolG]]-[[iolH]]-[[iolJ]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/9226270 PubMed]
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed], [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed1] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed2]  
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/9226270 PubMed]
  
−
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed], induced by heat ([[CtsR]]) [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]
+
* '''Regulation:'''  
−
** repressed at low temperatures ([[CtsR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/9987115 PubMed]
+
** repressed in the absence of inositol ([[IolR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/9887260 PubMed]
 +
** repressed by glucose ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10666464 PubMed]  
 +
** induced by inositol ([[IolR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/9226270 PubMed]
  
−
* '''Regulatory mechanism:''' [[CtsR]]: transcription repression [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]
+
* '''Regulatory mechanism:'''  
−
** [[CtsR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/9987115 PubMed]
+
** [[IolR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/9887260 PubMed]
 +
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10666464 PubMed]
 +
** [[IolR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/9226270 PubMed]
  
 
* '''Additional information:'''
 
* '''Additional information:'''
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
* [[Yasutaro Fujita]], University of Fukuyama, Japan
 +
* [[Ken-ichi Yoshida]], Kobe University, Japan
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>9987115, 19498169 ,11544224, </pubmed>
+
<pubmed>9887260,18310071, </pubmed>
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
# Yoshida K, Yamaguchi M, Morinaga T, Kinehara M, Ikeuchi M, Ashida H, Fujita Y. (2008) myo-Inositol catabolism in Bacillus subtilis. ''J Biol Chem. '' ''' Apr 18;283(16):''' 10415-24. [http://www.ncbi.nlm.nih.gov/sites/entrez/18310071 PubMed]

Revision as of 19:18, 12 June 2009

  • Description: formation of 2-deoxy-5-keto-gluconic acid (4th reaction)

Gene name iolB
Synonyms yxdB
Essential no
Product formation of 2-deoxy-5-keto-gluconic acid (4th reaction)
Function myo-inositol catabolism
Metabolic function and regulation of this protein in SubtiPathways:
Sugar catabolism
MW, pI 30 kDa, 4.77
Gene length, protein length 813 bp, 271 aa
Immediate neighbours iolC, iolA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
IolB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU39750

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: 5-deoxy-glucuronic acid = 5-dehydro-2-deoxy-D-gluconic acid (according to Swiss-Prot)
  • Protein family: isomerase iolB family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • 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

Ken-ichi Yoshida, Masanori Yamaguchi, Tetsuro Morinaga, Masaki Kinehara, Maya Ikeuchi, Hitoshi Ashida, Yasutaro Fujita
myo-Inositol catabolism in Bacillus subtilis.
J Biol Chem: 2008, 283(16);10415-24
[PubMed:18310071] [WorldCat.org] [DOI] (P p)

K I Yoshida, T Shibayama, D Aoyama, Y Fujita
Interaction of a repressor and its binding sites for regulation of the Bacillus subtilis iol divergon.
J Mol Biol: 1999, 285(3);917-29
[PubMed:9887260] [WorldCat.org] [DOI] (P p)


  1. Yoshida K, Yamaguchi M, Morinaga T, Kinehara M, Ikeuchi M, Ashida H, Fujita Y. (2008) myo-Inositol catabolism in Bacillus subtilis. J Biol Chem. Apr 18;283(16): 10415-24. PubMed
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