Difference between revisions of "Sandbox"

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* '''Description:''' 6-phosphogluconate dehydrogenase <br/><br/>
+
* '''Description:''' chaperonin and co-repressor for [[HrcA]]<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'''
−
|''gntZ''
+
|''groEL''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || 6-phosphogluconate dehydrogenase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || chaperonin, co-repressor for [[HrcA]]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || gluconate utilization
+
|style="background:#ABCDEF;" align="center"|'''Function''' || protein folding and re-folding
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 51 kDa, 4.756  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 57 kDa, 4.531  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1404 bp, 468 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1632 bp, 544 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gntP]]'', ''[[ahpC]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[groES]]'', ''[[ydiM]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16045&#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:CAB12422&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:gntZ_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:groEL_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:''' BSU40080
+
* '''Locus tag:''' BSU06030
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gntRKPZ.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/groESL.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10651]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10423]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== 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:''' acts as co-repressor for [[HrcA]]
  
−
* '''Protein family:''' 6-phosphogluconate dehydrogenase family (according to Swiss-Prot)
+
* '''Protein family:''' chaperonin (HSP60) family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 64: Line 66:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[HrcA]]-[[GroEL]],  [[GroEL]]-[[GroES]]
  
−
* '''Localization:'''
+
* '''Localization:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P12013 P12013]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P28598 P28598]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40080]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU06030]
  
−
* '''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:''' ''[[gntR]]-[[gntK]]-[[gntP]]-[[gntZ]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/10746760 PubMed1] [http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed2]
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed]
+
* '''[[Sigma factor]]:'''  
  
 
* '''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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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Wolfgang Schumann]], Bayreuth University, Germany [http://www.genetik.uni-bayreuth.de/LSGenetik1/schumann_research.htm Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 122: Line 122:
 
=References=
 
=References=
  
−
<pubmed>3020045 1659648, </pubmed>
+
<pubmed>17726680 16493705 9303302, </pubmed>
−
 
+
# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. ''Proteomics'' '''7:''' 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
−
 
+
# L&#233;vine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. ''Proteomics'' '''6:''' 2157-2173 [http://www.ncbi.nlm.nih.gov/pubmed/16493705 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]
+
# Mogk, A., Homuth, G., Scholz, C., Kim, L., Schmid, F. X., and Schumann, W. (1997) The GroE chaperonin machine is a major modulator of the CIRCE heat shock regulon of Bacillus subtilis. EMBO J 16, 4579-4590. [http://www.ncbi.nlm.nih.gov/sites/entrez/9303302 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]
 
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 14:06, 8 June 2009

  • Description: chaperonin and co-repressor for HrcA

Gene name groEL
Synonyms
Essential yes PubMed
Product chaperonin, co-repressor for HrcA
Function protein folding and re-folding
MW, pI 57 kDa, 4.531
Gene length, protein length 1632 bp, 544 aa
Immediate neighbours groES, ydiM
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
GroEL context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU06030

Phenotypes of a mutant

essential PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: acts as co-repressor for HrcA
  • Protein family: chaperonin (HSP60) family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylated on ser/ thr/ tyr PubMed, PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization: cytoplasm (according to Swiss-Prot)

Database entries

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

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Wolfgang Schumann, Bayreuth University, Germany Homepage

Your additional remarks

References

Christine Eymann, Dörte Becher, Jörg Bernhardt, Katrin Gronau, Anja Klutzny, Michael Hecker
Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis.
Proteomics: 2007, 7(19);3509-26
[PubMed:17726680] [WorldCat.org] [DOI] (P p)

Alain Lévine, Françoise Vannier, Cédric Absalon, Lauriane Kuhn, Peter Jackson, Elaine Scrivener, Valérie Labas, Joëlle Vinh, Patrick Courtney, Jérôme Garin, Simone J Séror
Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes.
Proteomics: 2006, 6(7);2157-73
[PubMed:16493705] [WorldCat.org] [DOI] (P p)

A Mogk, G Homuth, C Scholz, L Kim, F X Schmid, W Schumann
The GroE chaperonin machine is a major modulator of the CIRCE heat shock regulon of Bacillus subtilis.
EMBO J: 1997, 16(15);4579-90
[PubMed:9303302] [WorldCat.org] [DOI] (P p)

  1. Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis. Proteomics 7: 3509-3526. PubMed
  2. Lévine et al. (2006) Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6: 2157-2173 PubMed
  3. Mogk, A., Homuth, G., Scholz, C., Kim, L., Schmid, F. X., and Schumann, W. (1997) The GroE chaperonin machine is a major modulator of the CIRCE heat shock regulon of Bacillus subtilis. EMBO J 16, 4579-4590. PubMed
  4. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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