Difference between revisions of "Rnz"

From SubtiWiki
Jump to: navigation, search
(→‎Original Publications)
 
(44 intermediate revisions by 5 users not shown)
Line 1: Line 1:
−
* '''Description:''' RNase Z<br/><br/>
+
* '''Description:''' [[RNase]] Z<br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
Line 12: Line 12:
 
|style="background:#ABCDEF;" align="center"| '''Product''' || endoribonuclease Z
 
|style="background:#ABCDEF;" align="center"| '''Product''' || endoribonuclease Z
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || processing of CCA-less tRNA precursors
 +
|-
 +
|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   
Line 18: Line 20:
 
|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  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||  
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rpmGC]]'', ''[[zwf]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yqjK_nucleotide.txt    Gene sequence     (+200bp)  ]'''
+
|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]
−
|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=
Line 35: Line 49:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''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]
Line 46: Line 63:
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=The protein=
 
=The protein=
Line 53: Line 69:
  
 
* '''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:'''
+
* '''Protein family:''' [[RNase]] Z family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 70: Line 88:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''[[SubtInteract|Interactions]]:'''
  
−
* '''Localization:'''
+
* '''[[Localization]]:'''
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU23840&redirect=T BSU23840]
  
−
* '''Structure:'''
+
* '''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]
  
−
* '''Swiss prot entry:'''
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P54548 P54548]
  
−
* '''KEGG entry:'''
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23840]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 88: Line 107:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''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:'''  
Line 96: Line 117:
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''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 =
−
 
 
* '''Mutant:'''
 
* '''Mutant:'''
  
Line 119: Line 143:
  
 
=References=
 
=References=
 +
==Reviews==
 +
<pubmed> 19215776 17599240 25878039</pubmed>
 +
 +
==Original Publications==
 +
<pubmed>17005971 12941704 15654328 16518398 22940585 25402410  24022488</pubmed>
  
−
# Hunt, A., Rawlins, J. P., Thomaides, H. B., and Errington, J. (2006) Functional analysis of 11 putative essential genes in Bacillus subtilis. Microbiology 152, 2895-2907. [http://www.ncbi.nlm.nih.gov/sites/entrez/17005971 PubMed]
+
[[Category:Protein-coding genes]]
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 

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

Murray P Deutscher
How bacterial cells keep ribonucleases under control.
FEMS Microbiol Rev: 2015, 39(3);350-61
[PubMed:25878039] [WorldCat.org] [DOI] (I p)

Roland K Hartmann, Markus Gössringer, Bettina Späth, Susan Fischer, Anita Marchfelder
The making of tRNAs and more - RNase P and tRNase Z.
Prog Mol Biol Transl Sci: 2009, 85;319-68
[PubMed:19215776] [WorldCat.org] [DOI] (P p)

B Späth, G Canino, A Marchfelder
tRNase Z: the end is not in sight.
Cell Mol Life Sci: 2007, 64(18);2404-12
[PubMed:17599240] [WorldCat.org] [DOI] (P p)


Original Publications

Laetitia Gilet, Jeanne M DiChiara, Sabine Figaro, David H Bechhofer, Ciarán Condon
Small stable RNA maturation and turnover in Bacillus subtilis.
Mol Microbiol: 2015, 95(2);270-82
[PubMed:25402410] [WorldCat.org] [DOI] (I p)

Tanmay Dutta, Arun Malhotra, Murray P Deutscher
How a CCA sequence protects mature tRNAs and tRNA precursors from action of the processing enzyme RNase BN/RNase Z.
J Biol Chem: 2013, 288(42);30636-30644
[PubMed:24022488] [WorldCat.org] [DOI] (I p)

Olivier Pellegrini, Inés Li de la Sierra-Gallay, Jérémie Piton, Laetitia Gilet, Ciarán Condon
Activation of tRNA maturation by downstream uracil residues in B. subtilis.
Structure: 2012, 20(10);1769-77
[PubMed:22940585] [WorldCat.org] [DOI] (I 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)

Inés Li de la Sierra-Gallay, Nathalie Mathy, Olivier Pellegrini, Ciarán Condon
Structure of the ubiquitous 3' processing enzyme RNase Z bound to transfer RNA.
Nat Struct Mol Biol: 2006, 13(4);376-7
[PubMed:16518398] [WorldCat.org] [DOI] (P p)

Inés Li de la Sierra-Gallay, Olivier Pellegrini, Ciarán Condon
Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z.
Nature: 2005, 433(7026);657-61
[PubMed:15654328] [WorldCat.org] [DOI] (I p)

Olivier Pellegrini, Jamel Nezzar, Anita Marchfelder, Harald Putzer, Ciarán Condon
Endonucleolytic processing of CCA-less tRNA precursors by RNase Z in Bacillus subtilis.
EMBO J: 2003, 22(17);4534-43
[PubMed:12941704] [WorldCat.org] [DOI] (P p)

Retrieved from "http://subtiwiki-test.uni-goettingen.de/wiki//index.php?title=Rnz&oldid=207773"