Difference between revisions of "Rnz"

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* '''Description:''' RNase Z<br/><br/>
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* '''Description:''' [[RNase]] Z<br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqjK''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqjK''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' ||  
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|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Product''' || endoribonuclease Z
 
|style="background:#ABCDEF;" align="center"| '''Product''' || endoribonuclease Z
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
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|style="background:#ABCDEF;" align="center"|'''Function''' || processing of CCA-less tRNA precursors
 +
|-
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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=BSU23840 rnz]
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 5.805   
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 5.805   
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 921 bp, 307 aa  
 
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 921 bp, 307 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||  
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rpmGC]]'', ''[[zwf]]''
 
|-
 
|-
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yqjK_nucleotide.txt    Gene sequence     (+200bp)  ]'''
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|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU23840 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU23840 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU23840 DNA_with_flanks]
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yqjK_protein.txt Protein sequence]'''
 
 
|-
 
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:yqjK_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:yqjK_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=rnz_2478006_2478929_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:rnz_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU23840]]
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/>
 +
 +
= [[Categories]] containing this gene/protein =
 +
{{SubtiWiki category|[[Rnases]]}},
 +
{{SubtiWiki category|[[translation]]}},
 +
{{SubtiWiki category|[[essential genes]]}}
 +
 +
= This gene is a member of the following [[regulons]] =
  
−
<br/><br/>
 
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
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* '''Coordinates:'''
+
* '''Locus tag:''' BSU23840
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU23840&redirect=T BSU23840]
  
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqjK.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqjK.html]
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=== Additional information===
 
=== Additional information===
−
 
  
 
=The protein=
 
=The protein=
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
 +
** Endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs (according to Swiss-Prot)
 +
** 3' end maturation of tmRNA {{PubMed|25402410}}
  
−
* '''Protein family:'''
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* '''Protein family:''' [[RNase]] Z family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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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:'''
+
* '''[[Localization]]:'''
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU23840&redirect=T BSU23840]
  
−
* '''Structure:'''
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* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2FK6 2FK6] (in complex with tRNA-Thr) {{PubMed|22940585}},  [http://www.rcsb.org/pdb/explore.do?structureId=1Y44 1Y44]
  
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* '''Swiss prot entry:'''
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* '''UniProt:''' [http://www.uniprot.org/uniprot/P54548 P54548]
  
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* '''KEGG entry:'''
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* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23840]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
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* '''Operon:'''  
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* '''Operon:''' ''rnz'' (according to [http://dbtbs.hgc.jp/COG/prom/yqjK.html DBTBS])
 +
 
 +
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rnz_2478006_2478929_-1 rnz] {{PubMed|22383849}}
  
 
* '''Sigma factor:'''  
 
* '''Sigma factor:'''  
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* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
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* '''Additional information:'''  
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* '''Additional information:'''
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium): 55 {{PubMed|24696501}}
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 278 {{PubMed|21395229}}
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 379 {{PubMed|21395229}}
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 311 {{PubMed|21395229}}
  
 
=Biological materials =
 
=Biological materials =
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* '''Mutant:'''
 
* '''Mutant:'''
  
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=References=
 
=References=
 +
==Reviews==
 +
<pubmed> 19215776 17599240 25878039</pubmed>
 +
 +
==Original Publications==
 +
<pubmed>17005971 12941704 15654328 16518398 22940585 25402410  24022488</pubmed>
  
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# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
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[[Category:Protein-coding genes]]

Latest revision as of 15:09, 26 April 2015

Gene name rnz
Synonyms yqjK
Essential yes PubMed
Product endoribonuclease Z
Function processing of CCA-less tRNA precursors
Gene expression levels in SubtiExpress: rnz
MW, pI 33 kDa, 5.805
Gene length, protein length 921 bp, 307 aa
Immediate neighbours rpmGC, zwf
Sequences Protein DNA DNA_with_flanks
Genetic context
YqjK context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
Rnz expression.png















Categories containing this gene/protein

Rnases, translation, essential genes

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag: BSU23840

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:
    • Endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs (according to Swiss-Prot)
    • 3' end maturation of tmRNA PubMed
  • Protein family: RNase Z family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon: rnz (according to DBTBS)
  • Sigma factor:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:
    • number of protein molecules per cell (minimal medium with glucose and ammonium): 55 PubMed
    • number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 278 PubMed
    • number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 379 PubMed
    • number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 311 PubMed

Biological materials

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

Labs working on this gene/protein

Ciaran Condon, IBPC, Paris, France Homepage

Your additional remarks

References

Reviews


Original Publications

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