Difference between revisions of "Sandbox"

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* '''Description:''' Enzyme I, general (non sugar-specific) component of the PTS. Enzyme I transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein ([[PtsH |HPr]])  <br/><br/>
+
* '''Description:''' aminotransferase <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'''
−
|''ptsI''
+
|''patA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''uat ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || phosphotransferase system (PTS) enzyme I
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|style="background:#ABCDEF;" align="center"| '''Product''' || aminotransferase
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || PTS-dependent sugar transport
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|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of lysine and peptidoglycan
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62,9 kDa, 4.59
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 6.005 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1710 bp, 570 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1176 bp, 392 aa
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ptsH]]'', ''[[splA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[kinA]]'', ''[[cheV]]''
 
|-
 
|-
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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:CAB13264&#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:CAB13273&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:patA_context.gif]]
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|-
 
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|colspan="2" | '''Genetic context''' <br/> [[Image:ptsI_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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__TOC__
 
__TOC__
  
−
<br/><br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 1458959 - 1460668
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ptsGHI.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10201]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10205]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' PEP-dependent autophosphorylation on His-189, transfer of the phosphoryl group to [[PtsH |HPr]] (His-15)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' PEP-utilizing enzyme family
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
−
**HPr binding site (N-Terminal Domain)
 
−
**pyruvate binding site (C-Terminal Domain)
 
−
**pyrophosphate/phosphate carrier histidine (central Domain)
 
  
−
* '''Modification:''' transient autophosphorylation on His-189, in vivo also phosphorylated on Ser-34 or Ser-36 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
+
* '''Modification:'''
  
−
* '''Cofactor(s):''' Magnesium
+
* '''Cofactor(s):'''
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' Cytoplasm Cytoplasm
+
* '''Localization:''' Cytoplasm
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P08838]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU13910]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14000]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.3.9 2.7.3.9]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
 
* '''Operon:'''  
 
* '''Operon:'''  
−
**''[[ptsG]]-[[ptsH]]-[[ptsI]]''
 
−
**''[[ptsH]]-[[ptsI]]''
 
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11902727 PubMed]
+
* '''[[Sigma factor]]:'''  
−
* '''Regulation:''' expression activated by glucose (4.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  induction by glucose (''[[ptsG]]''), constitutive (''[[ptsH]]'')
+
 
 +
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' ''[[ptsG]]'': transcriptional antitermination via the [[GlcT]]-dependent RNA-switch
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP864 (ermC), available in [[Stülke]] lab
+
* '''Mutant:'''
  
−
* '''Expression vector:''' pAG3 (His-tag), available in [[Galinier]] lab
+
* '''Expression vector:'''
−
+
       
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
 +
 +
* '''two-hybrid system:'''
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Josef Deutscher]], Paris-Grignon, France
 
−
 
−
[[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
# 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]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Frisby, D., and Zuber, P. 1994. Mutations in pts cause catabolite-resistant sporulation and altered regulation of spo0H in Bacillus subtilis. J. Bacteriol. 176: 2587-2595. [http://www.ncbi.nlm.nih.gov/sites/entrez/8169206  PubMed]
 
−
# Macek B, Mijakovic I, Olsen JV (2007) The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis. ''Mol Cell Proteomics'' '''6(4):''' 697-707. [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
 

Revision as of 02:07, 30 April 2009

  • Description: aminotransferase

Gene name patA
Synonyms uat
Essential no
Product aminotransferase
Function biosynthesis of lysine and peptidoglycan
MW, pI 43 kDa, 6.005
Gene length, protein length 1176 bp, 392 aa
Immediate neighbours kinA, cheV
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
PatA 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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