Difference between revisions of "Sandbox"

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−
* '''Description:''' NH3-dependent NAD+ synthetase <br/><br/>
+
* '''Description:''' N-acetylglucosamine-6-phosphate deacetylase <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'''
−
|''nadE''
+
|''nagA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''outB, tscBGH, gsp-81 ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || NH3-dependent NAD+ synthetase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || N-acetylglucosamine-6-phosphate deacetylase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || NAD biosynthesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || N-acetylglucosamine utilization
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 4.888  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 5.276  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 816 bp, 272 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1188 bp, 396 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ycgI]]'', ''[[tmrB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[hprK]]'', ''[[nagB]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12107&#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:CAB15506&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:nadE_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:nagA_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:''' BSU03130
+
* '''Locus tag:''' BSU35010
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/nadE.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10694]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12630]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' ATP + deamido-NAD<sup>+</sup> + NH<sub>3</sub> = AMP + diphosphate + NAD<sup>+</sup> (according to Swiss-Prot)  
+
* '''Catalyzed reaction/ biological activity:''' N-acetyl-D-glucosamine 6-phosphate + H<sub>2</sub>O = D-glucosamine 6-phosphate + acetate (according to Swiss-Prot)  
  
−
* '''Protein family:''' NAD synthetase family (according to Swiss-Prot)
+
* '''Protein family:''' nagA family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 78: Line 76:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1KQP 1KQP]
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2VHL 2VHL]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08164 P08164]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34450 O34450]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU03130]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35010]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/6.3.1.5 6.3.1.5]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.5.1.25 3.5.1.25]
  
 
=== Additional information===
 
=== Additional information===
Line 92: Line 90:
 
* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
+
* '''Regulation:''' repressed by glucose (2.9-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression
  
 
* '''Additional information:'''  
 
* '''Additional information:'''  
Line 120: Line 118:
 
=References=
 
=References=
  
−
<pubmed>11544224, </pubmed>
+
<pubmed>12850135 6174502, </pubmed>
−
# Petersohn et al. (2001) Global Analysis of the General Stress Response of ''Bacillus subtilis''. ''J Bacteriol.'' '''183:''' 5617-5631 [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
+
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
 +
# Mobley HL, Doyle RJ, Streips UN, Langemeier SO. (1982) Transport and incorporation of N-acetyl-D-glucosamine in Bacillus subtilis. ''J Bacteriol. '' '''Apr;150(1):''' 8-15. [http://www.ncbi.nlm.nih.gov/sites/entrez/6174502 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 13:26, 8 June 2009

  • Description: N-acetylglucosamine-6-phosphate deacetylase

Gene name nagA
Synonyms
Essential no
Product N-acetylglucosamine-6-phosphate deacetylase
Function N-acetylglucosamine utilization
MW, pI 42 kDa, 5.276
Gene length, protein length 1188 bp, 396 aa
Immediate neighbours hprK, nagB
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
NagA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU35010

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: N-acetyl-D-glucosamine 6-phosphate + H2O = D-glucosamine 6-phosphate + acetate (according to Swiss-Prot)
  • Protein family: nagA 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:

Database entries

  • KEGG entry: [2]

Additional information

Expression and regulation

  • Operon:
  • Regulation: repressed by glucose (2.9-fold) (CcpA) PubMed
  • Regulatory mechanism: CcpA: transcription repression
  • 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

Hans-Matti Blencke, Georg Homuth, Holger Ludwig, Ulrike Mäder, Michael Hecker, Jörg Stülke
Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways.
Metab Eng: 2003, 5(2);133-49
[PubMed:12850135] [WorldCat.org] [DOI] (P p)

H L Mobley, R J Doyle, U N Streips, S O Langemeier
Transport and incorporation of N-acetyl-D-glucosamine in Bacillus subtilis.
J Bacteriol: 1982, 150(1);8-15
[PubMed:6174502] [WorldCat.org] [DOI] (P p)

  1. Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab Eng. 5: 133-149 PubMed
  2. Mobley HL, Doyle RJ, Streips UN, Langemeier SO. (1982) Transport and incorporation of N-acetyl-D-glucosamine in Bacillus subtilis. J Bacteriol. Apr;150(1): 8-15. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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