Difference between revisions of "Sandbox"

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−
* '''Description:''' 5-methylthioribose kinase <br/><br/>
+
* '''Description:''' NH3-dependent NAD+ synthetase <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'''
−
|''mtnK ''
+
|''nadE''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykrT''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''outB, tscBGH, gsp-81 ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || 5-methylthioribose kinase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || NH3-dependent NAD+ synthetase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || methionine salvage
+
|style="background:#ABCDEF;" align="center"|'''Function''' || NAD biosynthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 4.856  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 4.888  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1197 bp, 399 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 816 bp, 272 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mtnS]]'', ''[[mtnU]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ycgI]]'', ''[[tmrB]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13229&#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:CAB12107&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ykrT_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:nadE_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:''' BSU13560
+
* '''Locus tag:''' BSU03130
  
 
===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/mtnKA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/nadE.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13279]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10694]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' ATP + S-methyl-5-thio-D-ribose = ADP + S-methyl-5-thio-alpha-D-ribose 1-phosphate (according to Swiss-Prot)  
+
* '''Catalyzed reaction/ biological activity:''' ATP + deamido-NAD<sup>+</sup> + NH<sub>3</sub> = AMP + diphosphate + NAD<sup>+</sup> (according to Swiss-Prot)  
  
−
* '''Protein family:''' methylthioribose kinase family (according to Swiss-Prot)
+
* '''Protein family:''' NAD synthetase family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 72: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2PUP 2PUP]
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1KQP 1KQP]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31663 O31663]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08164 P08164]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU13560]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU03130]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.100 2.7.1.100]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/6.3.1.5 6.3.1.5]
  
 
=== Additional information===
 
=== Additional information===
−
 
−
:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[mtnK]]-[[mtnS]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11545674 PubMed]
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12022921 PubMed]
+
* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]  
  
−
* '''Regulation:''' induced by methionine starvation ([[S-box]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10094622 PubMed]
+
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
  
−
* '''Regulatory mechanism:''' [[S-box]]: transcription termination/ antitermination, the [[S-box]] [[riboswitch]] binds S-adenosylmethionine resulting in termination [http://www.ncbi.nlm.nih.gov/sites/entrez/10094622 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 120: Line 120:
 
=References=
 
=References=
  
−
<pubmed>18763711, </pubmed>
+
<pubmed>11544224, </pubmed>
−
# Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 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]
−
# 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]
 
 
# 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: NH3-dependent NAD+ synthetase

Gene name nadE
Synonyms outB, tscBGH, gsp-81
Essential yes PubMed
Product NH3-dependent NAD+ synthetase
Function NAD biosynthesis
MW, pI 30 kDa, 4.888
Gene length, protein length 816 bp, 272 aa
Immediate neighbours ycgI, tmrB
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
NadE context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU03130

Phenotypes of a mutant

essential PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: ATP + deamido-NAD+ + NH3 = AMP + diphosphate + NAD+ (according to Swiss-Prot)
  • Protein family: NAD synthetase 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: [3]

Additional information

Expression and regulation

  • Operon:
  • 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

A Petersohn, M Brigulla, S Haas, J D Hoheisel, U Völker, M Hecker
Global analysis of the general stress response of Bacillus subtilis.
J Bacteriol: 2001, 183(19);5617-31
[PubMed:11544224] [WorldCat.org] [DOI] (P p)

  1. Petersohn et al. (2001) Global Analysis of the General Stress Response of Bacillus subtilis. J Bacteriol. 183: 5617-5631 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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