Difference between revisions of "Sandbox"

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Test again, again.
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* '''Description:''' trigger enzyme: catabolic glutamate dehydrogenase induced by arginine, ornithine or proline, subject to carbon catabolite repression  <br/><br/>
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 +
{| align="right" border="1" cellpadding="2"
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|-
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|style="background:#ABCDEF;" align="center"|'''Gene name'''
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|''rocG''
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|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no
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|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || glutamate dehydrogenase (major)
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|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || arginine utilization, controls the activity of [[GltC]]
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|-
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|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/glutamate.html Ammonium/ glutamate]'''
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|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46.2 kDa, 6.28
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|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1272 bp, 424 amino acids
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|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yweA]]'', ''[[rocA]]''
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|-
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|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15806&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
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|-
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|colspan="2" | '''Genetic context''' <br/> [[Image:rocG_context.gif]]
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<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
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|-
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|}
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 +
__TOC__
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<br/><br/><br/><br/><br/><br/>
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 +
 
 +
=The gene=
 +
 
 +
=== Basic information ===
 +
 
 +
* '''Locus tag:''' BSU37790
 +
 
 +
===Phenotypes of a mutant ===
 +
 
 +
Poor growth on complex media such as SP (sporulation medium). No growth in minimal media with arginine as the only carbon source. Rapid accumulation of suppressor mutants ([[gudB |''gudB1'']])
 +
 
 +
=== Database entries ===
 +
 
 +
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rocG.html]
 +
 
 +
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10621]
 +
 
 +
=== Additional information===
 +
 
 +
=The protein=
 +
 
 +
=== Basic information/ Evolution ===
 +
 
 +
* '''Catalyzed reaction/ biological activity:''' L-glutamate + H<sub>2</sub>O + NAD<sup>+</sup> = 2-oxoglutarate + NH<sub>3</sub> + NADH (according to Swiss-Prot) L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate + NH(3) + NADH, controls the activity of the [[GltC]] transcription activator [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]
 +
 
 +
* '''Protein family:''' Glu/Leu/Phe/Val dehydrogenases family (according to Swiss-Prot) Glu/Leu/Phe/Val dehydrogenases family
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 +
* '''Paralogous protein(s):''' [[GudB]]
 +
 
 +
=== Extended information on the protein ===
 +
 
 +
* '''Kinetic information:'''
 +
 
 +
* '''Domains:'''
 +
 
 +
* '''Modification:'''
 +
 
 +
* '''Cofactor(s):'''
 +
 
 +
* '''Effectors of protein activity:'''
 +
 
 +
* '''Interactions:''' RocG-[[GltC]], this interaction prevents transcription activation of the ''[[gltA]]-[[gltB]]'' operon by GltC [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]
 +
 
 +
* '''Localization:'''
 +
 
 +
=== Database entries ===
 +
 
 +
* '''Structure:'''
 +
 
 +
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39633 P39633]
 +
 
 +
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37790]
 +
 
 +
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.4.1.2 1.4.1.2]  1.4.1.2]
 +
 
 +
=== Additional information===
 +
 
 +
 
 +
=Expression and regulation=
 +
 
 +
* '''Operon:''' ''rocG''
 +
 
 +
* '''Sigma factor:''' [[SigL]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10468601 PubMed]
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 +
* '''Regulation:''' induced by arginine ([[RocR]], [[AhrC]]), ornithine or proline, subject to carbon catabolite repression ([[CcpA]])
 +
 
 +
* '''Regulatory mechanism:''' [[RocR]]: transcription activation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12634342 PubMed][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10468601 PubMed]; [[AhrC]]: transcription activation ; [[CcpA]]: transcription repression
 +
 
 +
* '''Additional information:'''
 +
Activation by [[RocR]] requires binding of RocG to a downstream element [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12634342 PubMed]
 +
 
 +
=Biological materials =
 +
 
 +
* '''Mutant:''' GP747 (spc), GP726 (aphA3), GP810 (tet) available in [[Stülke]] lab
 +
 
 +
* '''Expression vector:'''
 +
** expression of native ''rocG'' in ''B. subtilis'': pGP529 (in [[pBQ200]]), available in [[Stülke]] lab
 +
** for purification of RocG carrying an N-terminal Strep-tag: pGP902 (in [[pGP172]]), a series of ''rocG'' variants is also available in [[pGP172]], available in [[Stülke]] lab
 +
 +
* '''lacZ fusion:'''
 +
 
 +
* '''GFP fusion:'''
 +
 
 +
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
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 +
* '''Antibody:''' available in [[Stülke]] lab
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 +
=Labs working on this gene/protein=
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 +
[[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
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[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
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 +
=Your additional remarks=
 +
 
 +
=References=
 +
 
 +
'''Enzymatic activity of RocG'''
 +
<pubmed>18603778,,16244435 16195607 ,18326565, 9829940  </pubmed>
 +
 +
'''Function in the control of [[GltC]] activity'''
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<pubmed>15150225,17994626 ,17608797 17183217  </pubmed>
 +
 
 +
'''Expression of ''rocG'''''
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<pubmed>12634342,15150224 10468601 9829940  </pubmed>
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 +
'''Structural analysis of glutamate dehydrogenase'''
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<pubmed>8263917 </pubmed>

Revision as of 15:26, 16 July 2009

  • Description: trigger enzyme: catabolic glutamate dehydrogenase induced by arginine, ornithine or proline, subject to carbon catabolite repression

Gene name rocG
Synonyms
Essential no
Product glutamate dehydrogenase (major)
Function arginine utilization, controls the activity of GltC
Metabolic function and regulation of this protein in SubtiPathways:
Ammonium/ glutamate
MW, pI 46.2 kDa, 6.28
Gene length, protein length 1272 bp, 424 amino acids
Immediate neighbours yweA, rocA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
RocG context.gif
This image was kindly provided by SubtiList








The gene

Basic information

  • Locus tag: BSU37790

Phenotypes of a mutant

Poor growth on complex media such as SP (sporulation medium). No growth in minimal media with arginine as the only carbon source. Rapid accumulation of suppressor mutants (gudB1)

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: L-glutamate + H2O + NAD+ = 2-oxoglutarate + NH3 + NADH (according to Swiss-Prot) L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate + NH(3) + NADH, controls the activity of the GltC transcription activator PubMed
  • Protein family: Glu/Leu/Phe/Val dehydrogenases family (according to Swiss-Prot) Glu/Leu/Phe/Val dehydrogenases family
  • Paralogous protein(s): GudB

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions: RocG-GltC, this interaction prevents transcription activation of the gltA-gltB operon by GltC PubMed
  • Localization:

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Operon: rocG
  • Regulation: induced by arginine (RocR, AhrC), ornithine or proline, subject to carbon catabolite repression (CcpA)
  • Regulatory mechanism: RocR: transcription activation PubMedPubMed; AhrC: transcription activation ; CcpA: transcription repression
  • Additional information:

Activation by RocR requires binding of RocG to a downstream element PubMed

Biological materials

  • Mutant: GP747 (spc), GP726 (aphA3), GP810 (tet) available in Stülke lab
  • Expression vector:
    • expression of native rocG in B. subtilis: pGP529 (in pBQ200), available in Stülke lab
    • for purification of RocG carrying an N-terminal Strep-tag: pGP902 (in pGP172), a series of rocG variants is also available in pGP172, available in Stülke lab
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab
  • Antibody: available in Stülke lab

Labs working on this gene/protein

Linc Sonenshein, Tufts University, Boston, MA, USA Homepage

Jörg Stülke, University of Göttingen, Germany Homepage

Your additional remarks

References

Enzymatic activity of RocG


Function in the control of GltC activity


Expression of rocG


Structural analysis of glutamate dehydrogenase

T J Stillman, P J Baker, K L Britton, D W Rice
Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis.
J Mol Biol: 1993, 234(4);1131-9
[PubMed:8263917] [WorldCat.org] [DOI] (P p)

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