Difference between revisions of "Sandbox"

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* '''Description:''' small subunit of glutamate synthase<br/><br/>
+
* '''Description:''' pyrroline-5-carboxylate reductase <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'''
−
|''gltB''
+
|''proH''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yoxE ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || glutamate synthase (small subunit)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || pyrroline-5-carboxylate reductase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || glutamate biosynthesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of proline
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 54.6 kDa, 7.69
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 7.754 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1479 bp, 493 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 891 bp, 297 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gltA]]'', ''[[yogA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[proJ]]'', ''[[rtp]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13727&#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:CAB13741&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:proH_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:gltB_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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<br/><br/>
 
<br/><br/>
−
 
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 2007785 - 2009263
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
auxotrophic for glutamate
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gltAB.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12594]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11049]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 56: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' 2 L-glutamate + NADP(+) <=> L-glutamine + 2-oxoglutarate + NADPH
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' glutamate synthase family.
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' none
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Domains:'''  
 
* '''Domains:'''  
−
** nucleotide binding domain (NADP) (299–313)
 
  
 
* '''Modification:'''
 
* '''Modification:'''
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34399]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU18440]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU18480]
  
−
* '''E.C. number:''' [http://www.expasy.ch/cgi-bin/get-enzyme-entry?1.4.1.13 1.4.1.13]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
  
 +
=Expression and regulation=
  
−
=Expression and regulation=
+
* '''Operon:'''
  
−
* '''Operon:''' ''[[gltA]]-[[gltB]]''
+
* '''[[Sigma factor]]:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]]
+
* '''Regulation:'''  
  
−
* '''Regulation:''' see ''[[gltA]]''
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP807 (del ''gltAB''::''tet''), GP736 (spc), available in [[Stülke]] lab
+
* '''Mutant:'''
  
−
* '''Expression vector:''' pGP1119 (in [[pGP380]], for SPINE, expression in ''B. subtilis''), available in [[Stülke]] lab
+
* '''Expression vector:'''
−
+
       
−
* '''lacZ fusion:''' see ''[[gltA]]''
+
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
 +
 +
* '''two-hybrid system:'''
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]
 
−
 
−
[[Stülke|Jörg Stülke]], University of Göttingen, Germany
 
−
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 125: Line 118:
 
=References=
 
=References=
  
−
# Yoshida K, et al. (2003) Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA box. ''Mol Microbiol'' '''49(1):''' 157-65. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12823818 PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Belitsky, B. R., and Sonenshein, A. L. (1995) Mutations in GltC that increase ''Bacillus subtilis gltA'' expression. J Bacteriol 177: 5696-5700.[http://www.ncbi.nlm.nih.gov/sites/entrez/7559360 PubMed]
 
−
# Belitsky, B. R., and Sonenshein, A. L. (2004) Modulation of activity of ''Bacillus subtilis'' regulatory proteins GltC and TnrA by glutamate dehydrogenase. J Bacteriol 186: 3399-3407.[http://www.ncbi.nlm.nih.gov/sites/entrez/15150225 PubMed]
 
−
# Bohannon, D. E., and Sonenshein, A. L. (1989) Positive regulation of glutamate biosynthesis in ''Bacillus subtilis''. J Bacteriol 171: 4718-4727.[http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]
 
−
# Commichau, F. M., Wacker, I., Schleider, J., Blencke, H.-M., Reif, I., Tripal, P., and Stülke, J. (2007) Characterization of ''Bacillus subtilis'' mutants with carbon source-independent glutamate biosynthesis. J Mol Microbiol Biotechnol 12: 106-113. [http://www.ncbi.nlm.nih.gov/sites/entrez/17183217 PubMed]
 
−
# Commichau, F. M., Herzberg, C., Tripal, P., Valerius, O., and Stülke, J. (2007) A regulatory protein-protein interaction governs glutamate biosynthesis in ''Bacillus subtilis'': The glutamate dehydrogenase RocG moonlights in controlling the transcription factor GltC. Mol Microbiol 65: 642-654. [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed] 
 
−
# Picossi, S., Belitsky, B. R., and Sonenshein, A. L. (2007) Molecular mechanism of the regulation of ''Bacillus subtilis gltAB'' expression by GltC. J Mol Biol 365: 1298-1313. [http://www.ncbi.nlm.nih.gov/sites/entrez/17134717 PubMed]
 
−
# Wacker, I., Ludwig, H., Reif, I., Blencke, H. M., Detsch, C., and Stülke, J. (2003) The regulatory link between carbon and nitrogen metabolism in ''Bacillus subtilis'': regulation of the ''gltAB'' operon by the catabolite control protein CcpA. Microbiology 149: 3001-3009.[http://www.ncbi.nlm.nih.gov/sites/entrez/14523131 PubMed]
 
−
# Belitsky, B. R., Wray, L. V., Jr., Fisher, S. H., Bohannon, D. E. & Sonenshein, A. L. (2000). Role of TnrA in nitrogen source-dependent repression of ''Bacillus subtilis'' glutamate synthase gene expression. J Bacteriol 182, 5939-5947. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11029411 PubMed]
 
−
# Commichau, F. M., Gunka, K., Landmann, J. J. & Stülke, J. (2008) Glutamate metabolism in ''Bacillus subtilis'': Gene expression and enzyme activities evolved to avoid futile cycles and to allow rapid responses to perturbations in the system. J. Bacteriol. 190: 3557-3564. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+18326565 PubMed]
 

Revision as of 02:27, 30 April 2009

  • Description: pyrroline-5-carboxylate reductase

Gene name proH
Synonyms yoxE
Essential no
Product pyrroline-5-carboxylate reductase
Function biosynthesis of proline
MW, pI 31 kDa, 7.754
Gene length, protein length 891 bp, 297 aa
Immediate neighbours proJ, rtp
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
ProH context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

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:
  • Interactions:
  • Localization: Cytoplasm

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [2]
  • 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

Your additional remarks

References

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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