Difference between revisions of "QueD"

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* '''Description:''' 6-pyruvoyltetrahydropterin synthase, synthesis of the modified ribonukleotide queuosine <br/><br/>
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* '''Description:''' 6-pyruvoyltetrahydropterin synthase, synthesis of the modified ribonucleotide queuosine <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
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|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || tRNA modification
 
|style="background:#ABCDEF;" align="center"|'''Function''' || tRNA modification
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|-
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|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU13730 queD]
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 5.944   
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 5.944   
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[queC]]'', ''[[queE]]''
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[queC]]'', ''[[queE]]''
 
|-
 
|-
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|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13246&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
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|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU13730 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU13730 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU13730 DNA_with_flanks]
 
|-
 
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ykvK_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ykvK_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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|-
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|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=queD_1440100_1440549_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:queD_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU13730]]
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
  
 
<br/><br/>
 
<br/><br/>
 +
 +
= [[Categories]] containing this gene/protein =
 +
{{SubtiWiki category|[[translation]]}}
 +
 +
= This gene is a member of the following [[regulons]] =
 +
{{SubtiWiki regulon|[[preQ1 riboswitch]]}}
  
 
=The gene=
 
=The gene=
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=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU13730&redirect=T BSU13730]
  
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
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=== Additional information===
 
=== Additional information===
 +
 +
  
  
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
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* '''Interactions:'''
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* '''[[SubtInteract|Interactions]]:'''
  
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* '''Localization:'''
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* '''[[Localization]]:'''
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU13730&redirect=T BSU13730]
  
 
* '''Structure:'''
 
* '''Structure:'''
  
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* '''Swiss prot entry:'''
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* '''UniProt:''' [http://www.uniprot.org/uniprot/O31676 O31676]
  
 
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13730]
 
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13730]
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=Expression and regulation=
 
=Expression and regulation=
  
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* '''Operon:'''  
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* '''Operon:''' ''[[queC]]-[[queD]]-[[queE]]-[[queF]]'' {{PubMed|14660578}}
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 +
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=queD_1440100_1440549_1 queD] {{PubMed|22383849}}
  
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* '''[[Sigma factor]]:'''  
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* '''Sigma factor:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
 +
** repressed in the presence of queuosine ([[preQ1 riboswitch]]) {{PubMed|19285444}}
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
 +
** [[preQ1 riboswitch]]: transcriptional antitermination in the absence of queuosine {{PubMed|19285444}}
  
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* '''Additional information:'''  
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* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
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<pubmed>16411777,18259064,14660578,, </pubmed>
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<pubmed>16411777,18259064,14660578,19285444, 17384645 </pubmed>
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Latest revision as of 13:33, 2 April 2014

  • Description: 6-pyruvoyltetrahydropterin synthase, synthesis of the modified ribonucleotide queuosine

Gene name queD
Synonyms ykvK
Essential no
Product 6-pyruvoyltetrahydropterin synthase
Function tRNA modification
Gene expression levels in SubtiExpress: queD
MW, pI 16 kDa, 5.944
Gene length, protein length 447 bp, 149 aa
Immediate neighbours queC, queE
Sequences Protein DNA DNA_with_flanks
Genetic context
YkvK context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
QueD expression.png
























Categories containing this gene/protein

translation

This gene is a member of the following regulons

preQ1 riboswitch

The gene

Basic information

  • Locus tag: BSU13730

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:

Database entries

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

Additional information

Expression and regulation

  • Sigma factor:
  • 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

Mijeong Kang, Robert Peterson, Juli Feigon
Structural Insights into riboswitch control of the biosynthesis of queuosine, a modified nucleotide found in the anticodon of tRNA.
Mol Cell: 2009, 33(6);784-90
[PubMed:19285444] [WorldCat.org] [DOI] (I p)

Nenad Cicmil, Lu Shi
Crystallization and preliminary X-ray characterization of queD from Bacillus subtilis, an enzyme involved in queuosine biosynthesis.
Acta Crystallogr Sect F Struct Biol Cryst Commun: 2008, 64(Pt 2);119-22
[PubMed:18259064] [WorldCat.org] [DOI] (I p)

Adam Roth, Wade C Winkler, Elizabeth E Regulski, Bobby W K Lee, Jinsoo Lim, Inbal Jona, Jeffrey E Barrick, Ankita Ritwik, Jane N Kim, Rüdiger Welz, Dirk Iwata-Reuyl, Ronald R Breaker
A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain.
Nat Struct Mol Biol: 2007, 14(4);308-17
[PubMed:17384645] [WorldCat.org] [DOI] (P p)

Matthew R Schaab, Brett M Barney, Wilson A Francisco
Kinetic and spectroscopic studies on the quercetin 2,3-dioxygenase from Bacillus subtilis.
Biochemistry: 2006, 45(3);1009-16
[PubMed:16411777] [WorldCat.org] [DOI] (P p)

John S Reader, David Metzgar, Paul Schimmel, Valérie de Crécy-Lagard
Identification of four genes necessary for biosynthesis of the modified nucleoside queuosine.
J Biol Chem: 2004, 279(8);6280-5
[PubMed:14660578] [WorldCat.org] [DOI] (P p)

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