Difference between revisions of "QueF"

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m (YkvM moved to QueF)
 
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* '''Description:''' write here <br/><br/>
+
* '''Description:''' nitrile reductase (NADPH-dependent 7-cyano-7-deazaguanine reductase), synthesis of the modified ribonucleotide queuosine <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'''
−
|''ykvM''
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|''queF ''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''queF ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykvM''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' ||  
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' ||  
+
|style="background:#ABCDEF;" align="center"| '''Product''' || nitrile reductase
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || tRNA modification
 +
|-
 +
|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=BSU13750 queF]
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 19 kDa, 4.927   
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 19 kDa, 4.927   
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 495 bp, 165 aa  
 
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 495 bp, 165 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||  
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[queE]]'', ''[[ykvN]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ykvM_nucleotide.txt    Gene sequence     (+200bp)  ]'''
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU13750 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU13750 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU13750 DNA_with_flanks]
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ykvM_protein.txt Protein sequence]'''
 
 
|-
 
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ykvM_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ykvM_context.gif]]
 +
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 +
|-
 +
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=queF_1441291_1441788_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:queF_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU13750]]
 
|-
 
|-
 
|}
 
|}
  
 
__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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=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Locus tag:''' BSU13750
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU13750&redirect=T BSU13750]
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ykvM.html]
+
* '''DBTBS entry:''' no entry
  
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13315]
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13315]
  
 
=== Additional information===
 
=== Additional information===
 +
 +
  
  
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' 7-aminomethyl-7-carbaguanine + 2 NADP<sup>+</sup> = 7-cyano-7-carbaguanine + 2 NADPH (according to Swiss-Prot)
  
−
* '''Protein family:'''
+
* '''Protein family:''' QueF type 1 subfamily (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' active site Cys56 is S-bacillithiolated by NaOCl stress {{PubMed|22938038}}
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''[[SubtInteract|Interactions]]:'''
  
−
* '''Localization:'''
+
* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU13750&redirect=T BSU13750]
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=4F8b 4F8B] (covalent thioimide intermediate of the unimodular nitrile reductase [[QueF]]) {{PubMed|22787148}}
  
−
* '''Swiss prot entry:'''
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* '''UniProt:''' [http://www.uniprot.org/uniprot/O31678 O31678]
  
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* '''KEGG entry:'''
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* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13750]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.7.1.13 1.7.1.13]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
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* '''Operon:'''  
+
* '''Operon:''' ''[[queC]]-[[queD]]-[[queE]]-[[queF]]'' {{PubMed|14660578}}
 +
 
 +
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=queF_1441291_1441788_1 queF] {{PubMed|22383849}}
  
 
* '''Sigma factor:'''  
 
* '''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:'''  
+
* '''Additional information:'''
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium): 303 {{PubMed|24696501}}
 +
** number of protein molecules per cell (complex medium with amino acids, without glucose): 913 {{PubMed|24696501}}
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
<pubmed>22938038,14660578,15767583 16511203 ,17929836 19285444 17384645 22787148 </pubmed>
 +
 
 +
[[Category:Protein-coding genes]]

Latest revision as of 09:43, 17 April 2014

  • Description: nitrile reductase (NADPH-dependent 7-cyano-7-deazaguanine reductase), synthesis of the modified ribonucleotide queuosine

Gene name queF
Synonyms ykvM
Essential no
Product nitrile reductase
Function tRNA modification
Gene expression levels in SubtiExpress: queF
MW, pI 19 kDa, 4.927
Gene length, protein length 495 bp, 165 aa
Immediate neighbours queE, ykvN
Sequences Protein DNA DNA_with_flanks
Genetic context
YkvM context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
QueF 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: BSU13750

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: 7-aminomethyl-7-carbaguanine + 2 NADP+ = 7-cyano-7-carbaguanine + 2 NADPH (according to Swiss-Prot)
  • Protein family: QueF type 1 subfamily (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: active site Cys56 is S-bacillithiolated by NaOCl stress PubMed
  • Cofactor(s):
  • Effectors of protein activity:

Database entries

  • Structure: 4F8B (covalent thioimide intermediate of the unimodular nitrile reductase QueF) PubMed
  • KEGG entry: [2]

Additional information

Expression and regulation

  • Sigma factor:
  • Additional information:
    • number of protein molecules per cell (minimal medium with glucose and ammonium): 303 PubMed
    • number of protein molecules per cell (complex medium with amino acids, without glucose): 913 PubMed

Biological materials

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

Labs working on this gene/protein

Your additional remarks

References

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