Difference between revisions of "TsaE"

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|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU05910 ydiB]
 
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU05910 ydiB]
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/YdiB YdiB]
+
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/TsaE TsaE]
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 4.597   
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 4.597   
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 474 bp, 158 aa  
 
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 474 bp, 158 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[thiL]]'', ''[[ydiC]]''
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[thiL]]'', ''[[tsaB]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12410&#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:CAB12410&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
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* '''[[Localization]]:'''  
 
* '''[[Localization]]:'''  
** cytoplasm with the excepton of the nucleoid region  [http://www.ncbi.nlm.nih.gov/sites/entrez/19246765 PubMed]
+
** cytoplasm with the exception of the nucleoid region  [http://www.ncbi.nlm.nih.gov/sites/entrez/19246765 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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=Expression and regulation=
 
=Expression and regulation=
  
* '''Operon:'''  
+
* '''Operon:''' ''[[thiL]]-[[tsaE]]-[[tsaB]]-[[ydiD]]-[[tsaD]]'' {{PubMed|22383849}}
  
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ydiB_641654_642130_1 ydiB] {{PubMed|22383849}}
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ydiB_641654_642130_1 tsaE] {{PubMed|22383849}}
  
 
* '''Sigma factor:'''  
 
* '''Sigma factor:'''  
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=References=
 
=References=
  
<pubmed> 17005971, 19246765 23072323</pubmed>
+
<pubmed> 17005971, 19246765 23072323 22383849</pubmed>
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 11:24, 18 October 2012

  • Description: P-loop ATPase, required for threonyl carbamoyl adenosine (t6A) modification of tRNAs that pair with ANN codons in mRNA

Gene name ydiB
Synonyms
Essential no
Product tRNA modification enzyme
Function tRNA modification
Gene expression levels in SubtiExpress: ydiB
Interactions involving this protein in SubtInteract: TsaE
MW, pI 17 kDa, 4.597
Gene length, protein length 474 bp, 158 aa
Immediate neighbours thiL, tsaB
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YdiB context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
YdiB expression.png















Categories containing this gene/protein

translation

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag: BSU05910

Phenotypes of a mutant

reduced growth rate PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
    • biosynthesis of the threonylcarbamoyladenosine (t6A) residue at position 37 of ANN-decoding tRNAs using L-threonylcarbamoyl-AMP (TsaB-TsaD-TsaE) PubMed
  • Protein family: UPF0079 family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information: K(M) for ATP: 60 myM, V(max) 10 nmol/min PubMed
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:

Database entries

  • Structure:
  • KEGG entry: [2]
  • E.C. number:

Additional information

ATPase activity is required for in vivo function of the protein PubMed

Expression and regulation

  • Sigma factor:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
    • for expression/ purification from B. subtilis with N-terminal Strep-tag, for SPINE, in pGP380: pGP833, available in Stülke lab
    • for expression/ purification from E. coli with N-terminal His-tag, in pWH844: pGP841, available in Stülke lab
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

Charles T Lauhon
Mechanism of N6-threonylcarbamoyladenonsine (t(6)A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl-AMP.
Biochemistry: 2012, 51(44);8950-63
[PubMed:23072323] [WorldCat.org] [DOI] (I p)

Pierre Nicolas, Ulrike Mäder, Etienne Dervyn, Tatiana Rochat, Aurélie Leduc, Nathalie Pigeonneau, Elena Bidnenko, Elodie Marchadier, Mark Hoebeke, Stéphane Aymerich, Dörte Becher, Paola Bisicchia, Eric Botella, Olivier Delumeau, Geoff Doherty, Emma L Denham, Mark J Fogg, Vincent Fromion, Anne Goelzer, Annette Hansen, Elisabeth Härtig, Colin R Harwood, Georg Homuth, Hanne Jarmer, Matthieu Jules, Edda Klipp, Ludovic Le Chat, François Lecointe, Peter Lewis, Wolfram Liebermeister, Anika March, Ruben A T Mars, Priyanka Nannapaneni, David Noone, Susanne Pohl, Bernd Rinn, Frank Rügheimer, Praveen K Sappa, Franck Samson, Marc Schaffer, Benno Schwikowski, Leif Steil, Jörg Stülke, Thomas Wiegert, Kevin M Devine, Anthony J Wilkinson, Jan Maarten van Dijl, Michael Hecker, Uwe Völker, Philippe Bessières, Philippe Noirot
Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.
Science: 2012, 335(6072);1103-6
[PubMed:22383849] [WorldCat.org] [DOI] (I p)

Johanna C Karst, Anne-Emmanuelle Foucher, Tracey L Campbell, Anne-Marie Di Guilmi, David Stroebel, Chand S Mangat, Eric D Brown, Jean-Michel Jault
The ATPase activity of an 'essential' Bacillus subtilis enzyme, YdiB, is required for its cellular function and is modulated by oligomerization.
Microbiology (Reading): 2009, 155(Pt 3);944-956
[PubMed:19246765] [WorldCat.org] [DOI] (P p)

Alison Hunt, Joy P Rawlins, Helena B Thomaides, Jeff Errington
Functional analysis of 11 putative essential genes in Bacillus subtilis.
Microbiology (Reading): 2006, 152(Pt 10);2895-2907
[PubMed:17005971] [WorldCat.org] [DOI] (P p)