Difference between revisions of "Sandbox"

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−
* '''Description:''' two-component response regulator, regulation of degradative enzyme and genetic competence, involved in activation of capsule biosynthetic operon expression (together with [[SwrAA]]), non-phosphorylated DegU is required for swarming motility [http://www3.interscience.wiley.com/journal/122328658/abstract PubMed] <br/><br/>
+
* '''Description:''' uroporphyrinogen decarboxylase (uroporphyrinogen III) <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'''
−
|''degU''
+
|''hemE''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sacU, iep ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || two-component response regulator
+
|style="background:#ABCDEF;" align="center"| '''Product''' || uroporphyrinogen decarboxylase (uroporphyrinogen III)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of degradative enzyme and genetic competence
+
|style="background:#ABCDEF;" align="center"|'''Function''' || heme biosynthesis
−
of genetic competence
 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 5.602  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 39 kDa, 5.262  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 687 bp, 229 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1059 bp, 353 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yviA]]'', ''[[degS]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pbpF]]'', ''[[hemH]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15566&#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:CAB12852&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:degU_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:hemE_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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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU35490
+
* '''Locus tag:''' BSU10120
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 42: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/degSU.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/hemEHY.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10393]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10429]
  
 
=== Additional information===
 
=== Additional information===
Line 53: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' transcription activator of degradative enzyme genes (''[[sacB]]'' and ''[[degQ]]'') and of ''[[comK]]'' expression
+
* '''Catalyzed reaction/ biological activity:''' Uroporphyrinogen III = coproporphyrinogen + 4 CO<sub>2</sub> (according to Swiss-Prot)  
  
−
* '''Protein family:'''
+
* '''Protein family:''' uroporphyrinogen decarboxylase family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
−
 
−
=== Genes controlled by DegU ===
 
−
 
−
* '''Activation by DegU-P:''' ''[[degS]]-[[degU]]''
 
−
 
−
* '''Activation by DegU:''' ''[[epr]]'' [http://www3.interscience.wiley.com/journal/122328658/abstract PubMed]
 
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylated by [[DegS]] on Asp-56 [http://www.ncbi.nlm.nih.gov/sites/entrez/1901568 PubMed], this modulates DNA-binding activity
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 77: Line 70:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[DegU]]-[[RapG]],  [[DegS]]-[[DegU]]
+
* '''Interactions:'''
  
 
* '''Localization:''' cytoplasm (according to Swiss-Prot)
 
* '''Localization:''' cytoplasm (according to Swiss-Prot)
Line 83: Line 76:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2INF 2INF]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P13800 P13800]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P32395 P32395]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35490]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU10120]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.1.37 4.1.1.37]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''''' [[degS]]-[[degU]]''
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' induced in the presence of ammonium ([[TnrA]])
+
* '''Regulation:'''  
−
** repressed in the absence of good nitrogen sources (glutamine or ammonium) ([[TnrA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/18502860 PubMed]
 
  
−
* '''Regulatory mechanism:''' [[TnrA]]: repression, [[DegU]]: positive autoregulation
+
* '''Regulatory mechanism:'''  
−
** [[TnrA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/18502860 PubMed]
 
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>17850253,12471443,8878039,14563871,1901568,1321152,1459944,18194340,10908654,18502860,10094672,19389763,18414485,19420703,2428811,7746142,,18502860, 19389763, 19416356, 19118340 </pubmed>
+
<pubmed>1459957,, </pubmed>
 +
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 09:03, 13 June 2009

  • Description: uroporphyrinogen decarboxylase (uroporphyrinogen III)

Gene name hemE
Synonyms
Essential no
Product uroporphyrinogen decarboxylase (uroporphyrinogen III)
Function heme biosynthesis
MW, pI 39 kDa, 5.262
Gene length, protein length 1059 bp, 353 aa
Immediate neighbours pbpF, hemH
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
HemE context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU10120

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Uroporphyrinogen III = coproporphyrinogen + 4 CO2 (according to Swiss-Prot)
  • Protein family: uroporphyrinogen decarboxylase 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: cytoplasm (according to Swiss-Prot)

Database entries

  • KEGG entry: [3]

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

M Hansson, L Hederstedt
Cloning and characterization of the Bacillus subtilis hemEHY gene cluster, which encodes protoheme IX biosynthetic enzymes.
J Bacteriol: 1992, 174(24);8081-93
[PubMed:1459957] [WorldCat.org] [DOI] (P p)

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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