Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' probable spore coat protein <br/><br/>
+
* '''Description:''' hypoxanthin/ guanine permease <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'''
−
|''cotP''
+
|''pbuG''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydfT ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yebB ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || probable spore coat protein
+
|style="background:#ABCDEF;" align="center"| '''Product''' || hypoxanthin/ guanine permease
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || resistance of the spore
+
|style="background:#ABCDEF;" align="center"|'''Function''' || hypoxanthine and guanine uptake
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 4.56  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 8.808  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 429 bp, 143 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1320 bp, 440 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydfS]]'', ''[[ydgA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[guaA]]'', ''[[yebC]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12362&#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:CAB12456&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:cotP_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:pbuG_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>
 
|-
 
|-
Line 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU05550
+
* '''Locus tag:''' BSU06370
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ydgBA-cotP.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pbuG.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12167]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12811]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' small heat shock protein (HSP20) family (according to Swiss-Prot)
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[PbuO]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 72: Line 72:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2EEW 2EEW] (the pbuG riboswitch, U47c mutant, bound to hypoxanthine)
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P96698 P96698]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU05550]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU06370]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 88: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''pbuG''
  
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
 +
** repressed in the presence of purine nucleotides ([[PurR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/11591660 PubMed]
 +
** repressed by hypoxanthine and guanine, [[PurR]]-independent, ([[G-box]])[http://www.ncbi.nlm.nih.gov/sites/entrez/12923093 PubMed]
 +
** repressed in the presence of adenine or adenosine([[PurR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/2536750 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
 +
** [[PurR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/11591660 PubMed]
 +
** [[PurR]]: transcription repression (molecular inducer: PRPP) [http://www.ncbi.nlm.nih.gov/sites/entrez/2536750 PubMed]
 +
**[[G-box]]: transcription termination/ antitermination ([[riboswitch]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12923093 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 118: Line 124:
 
=References=
 
=References=
  
 +
<pubmed>11591660,18763711 12923093, </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/pubmed/18763711 PubMed]
 +
# Johansen et al. (2003) Definition of a second ''Bacillus subtilis pur'' regulon comprising the ''pur'' and ''xpt-pbuX'' operons plus ''pbuG'', ''nupG'' (''yxjA''), and ''pbuE'' (''ydhL''). ''J. Bacteriol.'' '''185:''' 5200-5209. [http://www.ncbi.nlm.nih.gov/sites/entrez/12923093 PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 20:56, 12 June 2009

  • Description: hypoxanthin/ guanine permease

Gene name pbuG
Synonyms yebB
Essential no
Product hypoxanthin/ guanine permease
Function hypoxanthine and guanine uptake
MW, pI 46 kDa, 8.808
Gene length, protein length 1320 bp, 440 aa
Immediate neighbours guaA, yebC
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
PbuG context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU06370

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): PbuO

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: membrane PubMed

Database entries

  • Structure: 2EEW (the pbuG riboswitch, U47c mutant, bound to hypoxanthine)
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon: pbuG
  • Regulation:
    • repressed in the presence of purine nucleotides (PurR) PubMed
    • repressed by hypoxanthine and guanine, PurR-independent, (G-box)PubMed
    • repressed in the presence of adenine or adenosine(PurR) PubMed
  • 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

Hannes Hahne, Susanne Wolff, Michael Hecker, Dörte Becher
From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches.
Proteomics: 2008, 8(19);4123-36
[PubMed:18763711] [WorldCat.org] [DOI] (I p)

Lars Engholm Johansen, Per Nygaard, Catharina Lassen, Yvonne Agersø, Hans H Saxild
Definition of a second Bacillus subtilis pur regulon comprising the pur and xpt-pbuX operons plus pbuG, nupG (yxjA), and pbuE (ydhL).
J Bacteriol: 2003, 185(17);5200-9
[PubMed:12923093] [WorldCat.org] [DOI] (P p)

H H Saxild, K Brunstedt, K I Nielsen, H Jarmer, P Nygaard
Definition of the Bacillus subtilis PurR operator using genetic and bioinformatic tools and expansion of the PurR regulon with glyA, guaC, pbuG, xpt-pbuX, yqhZ-folD, and pbuO.
J Bacteriol: 2001, 183(21);6175-83
[PubMed:11591660] [WorldCat.org] [DOI] (P p)

  1. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  2. Johansen et al. (2003) Definition of a second Bacillus subtilis pur regulon comprising the pur and xpt-pbuX operons plus pbuG, nupG (yxjA), and pbuE (ydhL). J. Bacteriol. 185: 5200-5209. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=92538"