Difference between revisions of "Sandbox"

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* '''Description:''' penicillin-binding protein 5*, D-alanyl-D-alanine carboxypeptidase <br/><br/>
+
* '''Description:''' pyridoxal-5'-phosphate synthase (synthase domain) <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'''
−
|''dacA''
+
|''pdxS''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yaaD ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || penicillin-binding protein 5*, <br/>D-alanyl-D-alanine carboxypeptidase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || pyridoxal-5'-phosphate synthase (synthase domain)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || carboxypeptidase
+
|style="background:#ABCDEF;" align="center"|'''Function''' || pyridoxal-5'-phosphate biosynthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 5.668  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 5.085  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1329 bp, 443 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 882 bp, 294 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[guaB]]'', ''[[pdxS]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dacA]]'', ''[[pdxT]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11786&#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:CAB11787&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:dacA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yaaD_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/>
  
 
=The gene=
 
=The gene=
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===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
auxotrophic for pyridoxal 5'-phosphate [http://www.ncbi.nlm.nih.gov/sites/entrez/14762015 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yaaDE.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10074]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10075]
  
 
=== Additional information===
 
=== Additional information===
Line 64: Line 66:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylated on STY [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 70: Line 72:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[PdxS]]-[[PdxT]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16030023 PubMed1] [http://www.ncbi.nlm.nih.gov/sites/entrez/14762015 PubMed2]
  
−
* '''Localization:''' secreted (according to Swiss-Prot),  membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [[PdxS]]-[[PdxT]] complex [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=43151 2NV2]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08750 P08750]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37527 P37527]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00100]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00110]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 88: Line 90:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[pdxS]]-[[pdxT]]''
  
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' negatively controlled by [[Spo0A]] [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 118: Line 120:
 
=References=
 
=References=
  
−
# 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]
+
# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. ''Proteomics'' '''7:''' 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
 +
# L&#233;vine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. ''Proteomics'' '''6:''' 2157-2173 [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
 +
# Molle et al. (2003) The Spo0A regulon of ''Bacillus subtilis''.''Mol. Microbiol.'' '''50:''' 1683-1701. [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
 +
# Raschle et al. (2005) On the two components of pyridoxal 5'-phosphate synthase from ''Bacillus subtilis''.''J. Biol. Chem.'' '''280:''' 32291-32300. [http://www.ncbi.nlm.nih.gov/sites/entrez/16030023 PubMed]
 +
# Belitsky (2004) Physical and enzymological interaction of ''Bacillus subtilis'' proteins required for ''de novo'' pyridoxal 5'-phosphate biosynthesis.''J. Bacteriol.'' '''186:''' 1191-1196. [http://www.ncbi.nlm.nih.gov/sites/entrez/14762015 PubMed]

Revision as of 16:23, 4 May 2009

  • Description: pyridoxal-5'-phosphate synthase (synthase domain)

Gene name pdxS
Synonyms yaaD
Essential no
Product pyridoxal-5'-phosphate synthase (synthase domain)
Function pyridoxal-5'-phosphate biosynthesis
MW, pI 31 kDa, 5.085
Gene length, protein length 882 bp, 294 aa
Immediate neighbours dacA, pdxT
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YaaD context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

auxotrophic for pyridoxal 5'-phosphate PubMed

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:
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization:

Database entries

  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and 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. Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis. Proteomics 7: 3509-3526. PubMed
  2. Lévine et al. (2006) Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6: 2157-2173 PubMed
  3. Molle et al. (2003) The Spo0A regulon of Bacillus subtilis.Mol. Microbiol. 50: 1683-1701. PubMed
  4. Raschle et al. (2005) On the two components of pyridoxal 5'-phosphate synthase from Bacillus subtilis.J. Biol. Chem. 280: 32291-32300. PubMed
  5. Belitsky (2004) Physical and enzymological interaction of Bacillus subtilis proteins required for de novo pyridoxal 5'-phosphate biosynthesis.J. Bacteriol. 186: 1191-1196. PubMed
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