Difference between revisions of "Sandbox"

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−
* '''Description:''' NADP-dependent phosphogluconate dehydrogenase <br/><br/>
+
* '''Description:''' transcriptional repressor of the gluconate operon <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'''
−
|''gndA''
+
|''gntR''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqjI''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || NADP-dependent phosphogluconate dehydrogenase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional repressor of the gluconate operon
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of gluconate utilization
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 51 kDa, 5.076  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 5.26  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1407 bp, 469 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 729 bp, 243 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[zwf]]'', ''[[polY1]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxaA]]'', ''[[gntK]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14318&#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:CAB16042&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yqjI_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:gntR_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:''' BSU23860
+
* '''Locus tag:''' BSU40050
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqjHI.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gntRKPZ.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11738]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10648]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' 6-phospho-D-gluconate + NADP<sup>+</sup> = D-ribulose 5-phosphate + CO<sub>2</sub> + NADPH (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' 6-phosphogluconate dehydrogenase family (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 64: Line 64:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation on (Thr-15 OR Thr-17) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:''' gluconate acts as molecular inducer
  
 
* '''Interactions:'''
 
* '''Interactions:'''
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80859 P80859]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P10585 P10585]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23860]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40050]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.44 1.1.1.44]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[gntR]]-[[gntK]]-[[gntP]]-[[gntZ]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/10746760 PubMed1][http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed2]
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
 +
**  induced by gluconate ([[GntR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed]
 +
** repressed by glucose ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/8370661 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
 +
** [[GntR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed]
 +
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10666464 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>17218307, </pubmed>
+
<pubmed>7476858 3020045 1659648, </pubmed>
−
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
+
# Yoshida K, Miwa Y, Ohmori H, Fujita Y. (1995) Analysis of an insertional operator mutation (gntOi) that affects the expression level of the Bacillus subtilis gnt operon, and characterization of gntOi suppressor mutations. ''Mol Gen Genet.'' '''Sep 20;248(5):''' 583-91. [http://www.ncbi.nlm.nih.gov/sites/entrez/7476858 PubMed]
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
# Fujita Y, Fujita T, Miwa Y, Nihashi J, Aratani Y. (1986) Organization and transcription of the gluconate operon, gnt, of Bacillus subtilis. ''J Biol Chem.'' '''Oct 15;261(29):''' 13744-53. [http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed]
 +
# Reizer A., Deutscher J., Saier M.H. Jr., Reizer J. (1991) Analysis of the gluconate (gnt) operon of Bacillus subtilis. ''Mol. Microbiol.'' '''5:''' 1081-1089. [http://www.ncbi.nlm.nih.gov/sites/entrez/1659648 PubMed]

Revision as of 13:19, 8 June 2009

  • Description: transcriptional repressor of the gluconate operon

Gene name gntR
Synonyms
Essential no
Product transcriptional repressor of the gluconate operon
Function regulation of gluconate utilization
MW, pI 28 kDa, 5.26
Gene length, protein length 729 bp, 243 aa
Immediate neighbours yxaA, gntK
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
GntR context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU40050

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity: gluconate acts as molecular inducer
  • 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

K Yoshida, Y Miwa, H Ohmori, Y Fujita
Analysis of an insertional operator mutation (gntOi) that affects the expression level of the Bacillus subtilis gnt operon, and characterization of gntOi suppressor mutations.
Mol Gen Genet: 1995, 248(5);583-91
[PubMed:7476858] [WorldCat.org] [DOI] (P p)

A Reizer, J Deutscher, M H Saier, J Reizer
Analysis of the gluconate (gnt) operon of Bacillus subtilis.
Mol Microbiol: 1991, 5(5);1081-9
[PubMed:1659648] [WorldCat.org] [DOI] (P p)

Y Fujita, T Fujita, Y Miwa, J Nihashi, Y Aratani
Organization and transcription of the gluconate operon, gnt, of Bacillus subtilis.
J Biol Chem: 1986, 261(29);13744-53
[PubMed:3020045] [WorldCat.org] (P p)

  1. Yoshida K, Miwa Y, Ohmori H, Fujita Y. (1995) Analysis of an insertional operator mutation (gntOi) that affects the expression level of the Bacillus subtilis gnt operon, and characterization of gntOi suppressor mutations. Mol Gen Genet. Sep 20;248(5): 583-91. PubMed
  2. Fujita Y, Fujita T, Miwa Y, Nihashi J, Aratani Y. (1986) Organization and transcription of the gluconate operon, gnt, of Bacillus subtilis. J Biol Chem. Oct 15;261(29): 13744-53. PubMed
  3. Reizer A., Deutscher J., Saier M.H. Jr., Reizer J. (1991) Analysis of the gluconate (gnt) operon of Bacillus subtilis. Mol. Microbiol. 5: 1081-1089. PubMed
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