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:''' write here <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'''
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|''ptsI''
+
|''dppB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dciAB ''
 
|-
 
|-
−
|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''' || dipeptide ABC transporter (permease)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || PTS-dependent sugar transport
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|style="background:#ABCDEF;" align="center"|'''Function''' ||  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62,9 kDa, 4.59
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 9.942 
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1710 bp, 570 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 924 bp, 308 aa
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ptsH]]'', ''[[splA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dppA]]'', ''[[dppC]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ptsI_nucleotide.txt    Gene sequence      (+200bp) ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dppB_nucleotide.txt    Gene sequence      (+200bp)   ]'''  
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ptsI_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dppB_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
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|colspan="2" | '''Genetic context''' <br/> [[Image:dppB_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ptsI_context.gif]]
 
 
|-
 
|-
 
|}
 
|}
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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:''' [http://dbtbs.hgc.jp/COG/prom/dppABCDE.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10201]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10843]
  
 
=== 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-44 or Ser-46 [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
+
* '''Localization:'''
  
 
=== 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:'''
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/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:''' induction by glucose (''[[ptsG]]''), constitutive (''[[ptsH]]'')
 
  
−
* '''Regulatory mechanism:''' ''[[ptsG]]'': transcriptional antitermination via the [[GlcT]]-dependent RNA-switch
+
* '''Regulation:'''  
  
−
* '''Additional information:'''
+
* '''Regulatory mechanism:'''
 +
 
 +
* '''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=
  
−
# 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]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID 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 16:53, 9 March 2009

  • Description: write here

Gene name dppB
Synonyms dciAB
Essential no
Product dipeptide ABC transporter (permease)
Function
MW, pI 33 kDa, 9.942
Gene length, protein length 924 bp, 308 aa
Immediate neighbours dppA, dppC
Gene sequence (+200bp) Protein sequence
Genetic context
DppB context.gif



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

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

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:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry:
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • 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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