Difference between revisions of "Sandbox"

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−
* '''Description:''' large subunit of glutamate synthase  <br/><br/>
+
* '''Description:''' similar to H+/glutamate symporter <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'''
−
|''gltA''
+
|''gltP''
 
|-
 
|-
 
|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''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || glutamate synthase (large subunit)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || glutamate biosynthesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 168 kDa, 5.47
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 44 kDa, 8.651 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 4560 bp, 1520 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1242 bp, 414 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gltC]]'', ''[[gltB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybfQ]]'', ''[[gamP]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13728&#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:CAB12028&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
 
|-
 
|-
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:gltA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:gltP_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=
Line 38: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU18450
+
* '''Locus tag:''' BSU02340
  
 
===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+BG10811]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11015]
  
 
=== Additional information===
 
=== Additional information===
Line 57: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' 2 L-glutamate + NADP<sup>+</sup> = L-glutamine + 2-oxoglutarate + NADPH (according to Swiss-Prot) 2 L-glutamate + NADP(+) <=> L-glutamine + 2-oxoglutarate + NADPH
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' glutamate synthase family (according to Swiss-Prot) glutamate synthase family
+
* '''Protein family:''' View classification (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):''' [[YerD]]
+
* '''Paralogous protein(s):''' [[GltT]], [[DctP]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 68: Line 65:
  
 
* '''Domains:'''  
 
* '''Domains:'''  
−
** Glutamine amidotransferase type-2 domain (22-415)
 
−
** Nucleotide binding domain (1060-1112)
 
  
 
* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):''' 3Fe-4S, FAD, FMN
+
* '''Cofactor(s):'''
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
Line 79: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' membrane associated [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+18763711 PubMed], cytoplasm
+
* '''Localization:''' cell membrane (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
Line 85: Line 80:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39812 P39812]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39817 P39817]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU18450]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU02340]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.4.1.13 1.4.1.13] 3 1.4.1.13]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
−
subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[gltA]]-[[gltB]]''
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' expression activated by glucose (11 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  induced by sugar [http://www.ncbi.nlm.nih.gov/sites/entrez/14523131 PubMed], repressed by arginine [http://www.ncbi.nlm.nih.gov/sites/entrez/15150225 PubMed], ammonium required [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11029411 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' Activator: [[GltC]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]; Repressor: [[TnrA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11029411 PubMed], pos. regulated by a mutant form of [[GltR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+9023181 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP807 (del ''gltAB''::''tet''), GP222 (''gltA'' under the control of p-xyl), available in [[Stülke]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
−
+
       
−
* '''lacZ fusion:''' pGP526 (in [[pAC7]]), pGP919 (in [[pAC5]]), available in [[Stülke]] lab
+
* '''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 133: Line 120:
 
=References=
 
=References=
  
−
<pubmed>12850135 7559360 15150225 2548995 17183217 17608797 17134717 14523131, </pubmed>
+
<pubmed>7751298, </pubmed>
−
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
+
# Tolner, B., Ubbink-Kok, T., Poolman, B. and Konings, W.N. 1995. Characterization of the proton/glutamate symport protein of Bacillus subtilis and its functional expression in Escherichia coli. J. Bacteriol. 177: 2863-2869. [http://www.ncbi.nlm.nih.gov/sites/entrez/7751298 PubMed]
−
# 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 BR, Sonenshein AL (1997) Altered transcription activation specificity of a mutant form of Bacillus subtilis GltR, a LysR family member. J Bacteriol 179:1035-1043 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11029411 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]
 
−
# Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 
−
# Hahne et al. (2008) From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8:4123-4136 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+18763711 PubMed]
 

Revision as of 14:05, 8 June 2009

  • Description: similar to H+/glutamate symporter

Gene name gltP
Synonyms
Essential no
Product unknown
Function unknown
MW, pI 44 kDa, 8.651
Gene length, protein length 1242 bp, 414 aa
Immediate neighbours ybfQ, gamP
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
GltP context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU02340

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: View classification (according to Swiss-Prot)

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cell membrane (according to Swiss-Prot)

Database entries

  • Structure:
  • 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

B Tolner, T Ubbink-Kok, B Poolman, W N Konings
Characterization of the proton/glutamate symport protein of Bacillus subtilis and its functional expression in Escherichia coli.
J Bacteriol: 1995, 177(10);2863-9
[PubMed:7751298] [WorldCat.org] [DOI] (P p)

  1. Tolner, B., Ubbink-Kok, T., Poolman, B. and Konings, W.N. 1995. Characterization of the proton/glutamate symport protein of Bacillus subtilis and its functional expression in Escherichia coli. J. Bacteriol. 177: 2863-2869. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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