Difference between revisions of "Sandbox"

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−
* '''Description:''' methylthioribulose-1-phosphate dehydratase <br/><br/>
+
* '''Description:''' 5-methylthioribose kinase <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'''
−
|''mtnB''
+
|''mtnK ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykrY''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykrT''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || methylthioribulose-1-phosphate dehydratase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || 5-methylthioribose kinase
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || methionine salvage
 
|style="background:#ABCDEF;" align="center"|'''Function''' || methionine salvage
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 5.686  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 4.856  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 627 bp, 209 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1197 bp, 399 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mtnX]]'', ''[[mtnD]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mtnS]]'', ''[[mtnU]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13234&#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:CAB13229&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ykrY_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ykrT_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:''' BSU13610
+
* '''Locus tag:''' BSU13560
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/mtnWXBD.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/mtnKA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13284]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13279]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' S-methyl-5-thio-D-ribulose 1-phosphate = 5-(methylthio)-2,3-dioxopentyl phosphate + H<sub>2</sub>O (according to Swiss-Prot)  
+
* '''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)  
  
−
* '''Protein family:''' MtnB subfamily (according to Swiss-Prot)
+
* '''Protein family:''' methylthioribose kinase family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2PUP 2PUP]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31668 O31668]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31663 O31663]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU13610]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU13560]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.109 4.2.1.109]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.100 2.7.1.100]
  
 
=== 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:''' ''[[mtnW]]-[[mtnX]]-[[mtnB]]-[[mtnD]]'' [http://www.ncbi.nlm.nih.gov/pubmed/12022921 PubMed]
+
* '''Operon:''' ''[[mtnK]]-[[mtnS]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11545674 PubMed]
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/12022921 PubMed]
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12022921 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' induced by methionine starvation ([[S-box]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10094622 PubMed]
−
**repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed] 
 
−
** induced by methionine starvation ([[S-box]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10094622 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:''' [[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]
  
−
* '''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]
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>12107147, </pubmed>
+
<pubmed>18763711, </pubmed>
−
# M&#228;der et al. (2002) Transcriptome and Proteome Analysis of ''Bacillus subtilis'' Gene Expression Modulated by Amino Acid Availability. ''J. Bacteriol'' '''184:''' 1844288-4295 [http://www.ncbi.nlm.nih.gov/pubmed/12107147 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]
 +
# 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 13:25, 8 June 2009

  • Description: 5-methylthioribose kinase

Gene name mtnK
Synonyms ykrT
Essential no
Product 5-methylthioribose kinase
Function methionine salvage
MW, pI 45 kDa, 4.856
Gene length, protein length 1197 bp, 399 aa
Immediate neighbours mtnS, mtnU
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YkrT context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU13560

Phenotypes of a mutant

Database entries

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

Additional information

The protein

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)
  • Protein family: methylthioribose kinase 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: membrane associated PubMed

Database entries

  • KEGG entry: [3]

Additional information

  • subject to Clp-dependent proteolysis upon glucose starvation PubMed

Expression and regulation

  • Regulation: induced by methionine starvation (S-box) PubMed
  • Regulatory mechanism: S-box: transcription termination/ antitermination, the S-box riboswitch binds S-adenosylmethionine resulting in termination PubMed
  • Additional information: subject to Clp-dependent proteolysis upon glucose starvation PubMed

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

Hannes Hahne, Susanne Wolff, Michael Hecker, Dörte Becher
From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches.
Proteomics: 2008, 8(19);4123-36
[PubMed:18763711] [WorldCat.org] [DOI] (I p)

  1. Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 PubMed
  2. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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