Difference between revisions of "Sandbox"

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* '''Description:''' nitrogen-regulated PII-like protein <br/><br/>
+
* '''Description:''' phytase <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'''
−
|''nrgB''
+
|''phy''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yodV, yzxA ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || nitrogen-regulated PII-like protein
+
|style="background:#ABCDEF;" align="center"| '''Product''' || 3-phytase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of ammonium uptake
+
|style="background:#ABCDEF;" align="center"|'''Function''' || untilization of inositol hexakisphosphate (phytate)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 12 kDa, 8.825  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 4.936  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 348 bp, 116 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1146 bp, 382 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[nrgA]]'', ''[[bcrC]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cgeB]]'', ''[[yodU]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/nrgB_nucleotide.txt    Gene sequence      (+200bp)  ]'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13871&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/nrgB_protein.txt Protein sequence]'''
 
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:nrgB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:phy_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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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/nrgAB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/phy.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10870]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11198]
  
 
=== Additional information===
 
=== Additional information===
Line 53: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' Myo-inositol hexakisphosphate + H<sub>2</sub>O = 1D-myo-inositol 1,2,4,5,6-pentakisphosphate + phosphate (according to Swiss-Prot)
  
−
* '''Protein family:''' P(II) protein family (according to Swiss-Prot)
+
* '''Protein family:''' msrA Met sulfoxide reductase family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[NrgA]]-[[NrgB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/14600241 PubMed], [[TnrA]]-[[NrgB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17001076 PubMed]
+
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot),  membrane
+
* '''Localization:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1QLG 1QLG] (enzyme from B. amyloliquefaciens, 72% identity)
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/Q07428 Q07428]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P42094 P42094]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU36520 BSU36520]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU19800 BSU19800]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.3.8 3.1.3.8]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[nrgA]]-[[nrgB]]''
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' induced by ammonium limitation
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' transcription activation by [[TnrA]]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
  
−
* '''Antibody:''' available in [[Jörg Stülke]] lab
+
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Susan Fisher]], Boston, USA [http://www.bumc.bu.edu/microbiology/research/susan-h-fisher-phd/ homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
# Atkinson MR, Fisher SH (1991) Identification of genes and gene products whose expression is activated during nitrogen-limited growth in Bacillus subtilis. J Bacteriol 173:23-27. [http://www.ncbi.nlm.nih.gov/sites/entrez/1670935 PubMed]
+
# Voigt et al. (2009) Cell physiology and protein secretion of ''Bacillus licheniformis'' compared to ''Bacillus subtilis''. ''J Mol Microbiol Biotechnol.'' '''16:''' 53-68 [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
−
# Wray, L. V., Atkinson, M. R. & Fisher, S. H. (1994). The nitrogen-regulated Bacillus subtilis nrgAB operon encodes a membrane protein and a protein highly similar to the Escherichia coli glnB-encoded PII protein. J Bacteriol 176, 108-114. [http://www.ncbi.nlm.nih.gov/sites/entrez/8282685 PubMed]
 
−
# Detsch, C. & Stülke, J. (2003) Ammonium utilization in ''Bacillus subtilis'': transport and regulatory functions of NrgA and NrgB. Microbiology 149: 3289-3297. [http://www.ncbi.nlm.nih.gov/sites/entrez/14600241 PubMed]
 
−
# Heinrich, A., Woyda, K., Brauburger, K., Meiss, G., Detsch, C., Stülke, J. & Forchhammer, K. (2006) Interaction of the membrane-bound GlnK-AmtB complex with the master regulator of nitrogen metabolism TnrA in ''Bacillus subtilis''. J. Biol. Chem. 281: 34909-34917. [http://www.ncbi.nlm.nih.gov/sites/entrez/17001076 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 14:31, 25 May 2009

  • Description: phytase

Gene name phy
Synonyms yodV, yzxA
Essential no
Product 3-phytase
Function untilization of inositol hexakisphosphate (phytate)
MW, pI 41 kDa, 4.936
Gene length, protein length 1146 bp, 382 aa
Immediate neighbours cgeB, yodU
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
Phy context.gif
This image was kindly provided by SubtiList



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: Myo-inositol hexakisphosphate + H2O = 1D-myo-inositol 1,2,4,5,6-pentakisphosphate + phosphate (according to Swiss-Prot)
  • Protein family: msrA Met sulfoxide reductase family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure: 1QLG (enzyme from B. amyloliquefaciens, 72% identity)

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. Voigt et al. (2009) Cell physiology and protein secretion of Bacillus licheniformis compared to Bacillus subtilis. J Mol Microbiol Biotechnol. 16: 53-68 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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