Difference between revisions of "Sandbox"

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* '''Description:''' tRNA specific adenosine deaminase<br/><br/>
+
* '''Description:''' 4.5 S RNA<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'''
−
|''yaaJ''
+
|''scr''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || tRNA specific adenosine deaminase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || small cytoplasmic RNA (scRNA, 4.5S RNA),
−
|-
+
 
−
|style="background:#ABCDEF;" align="center"|'''Function''' || tRNA modification
+
[[signal recognition particle]]-like ([[SRP]]) component
−
|-
 
−
|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=BSU00180 yaaJ]
 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 5.636 
+
|style="background:#ABCDEF;" align="center"|'''Function''' || presecretory protein translocation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 483 bp, 161 aa
+
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this RNA in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=Scr Scr]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaI]]'', ''[[scr]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaJ]]'', ''[[dnaX]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00180 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00180 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00180 DNA_with_flanks]
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/scr_nucleotide.txt    Gene sequence     (+200bp)  ]'''
 +
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/scr_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yaaJ_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:scr_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>
−
|-
 
−
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tadA_25852_26337_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yaaJ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00180]]
 
 
|-
 
|-
 
|}
 
|}
  
 
__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/><br/><br/>
−
<br/><br/>
 
  
 
= [[Categories]] containing this gene/protein =
 
= [[Categories]] containing this gene/protein =
−
{{SubtiWiki category|[[translation]]}}
+
{{SubtiWiki category|[[protein secretion]]}},
 +
{{SubtiWiki category|[[essential genes]]}},
 +
{{SubtiWiki category|[[ncRNA]]}}
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
Line 51: Line 44:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00180
+
* '''Locus tag:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
* the gene is essential {{PubMed|7506707}}
 +
=== Database entries ===
  
−
=== Database entries ===
+
* '''DBTBS entry:''' no entry
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yaaJ-scr.html]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG00095]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10082]
+
* '''Structure:'''
  
 
=== Additional information===
 
=== Additional information===
  
  
−
 
+
=The RNA=
−
 
 
−
=The protein=
 
  
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' cytidine and deoxycytidylate deaminase family (according to Swiss-Prot)
+
=== Extended information on the RNA===
−
 
 
−
* '''Paralogous protein(s):'''
 
−
 
 
−
* '''The corresponding gene in ''E. coli'':''' [http://ecoliwiki.net/colipedia/index.php/tadA EcoliWiki]
 
−
 
 
−
=== Extended information on the protein ===
 
−
 
 
−
* '''Kinetic information:'''
 
−
 
 
−
* '''Domains:'''
 
−
 
 
−
* '''Modification:'''
 
−
 
 
−
* '''Cofactor(s):'''
 
  
−
* '''Effectors of protein activity:'''
+
* '''Kinetic information'''
  
−
* '''[[SubtInteract|Interactions]]:'''
+
* '''[[SubtInteract|Interactions]]:'''  
 +
** [[Scr]]-[[Ffh]] in the [[signal recognition particle]]
  
−
* '''[[Localization]]:'''
+
* '''[[Localization]]'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2B3J 2B3J] (the protein of ''Staphylococcus aureus'', complex with RNA) {{PubMed|16415880}}
+
* '''Structure''':  
−
 
 
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/P21335 P21335]
 
−
 
 
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00180]
 
−
 
 
−
* '''E.C. number:''' [http://www.chem.qmul.ac.uk/iubmb/enzyme/EC3/5/4/ 3.5.4.-]
 
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''''' [[yaaJ]]-[[scr]]''
+
* '''Operon:''' ''[[yaaJ]]-[[scr]],  [[scr]]''
  
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tadA_25852_26337_1 yaaJ] {{PubMed|22383849}}
+
* '''Sigma factor:''' [[SigA]] (both promoters)
−
 
 
−
* '''Sigma factor:''' [[SigA]]
 
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 118: Line 90:
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:''' transcribed as 354 nt precursor, cleaved at the 5' end by [[rnc| RNase III]] and at the 3' site by [[rnjA| RNase J1]] to yield a 275 nt molecule, final trimming to 271 nt sc RNA by [[rph| RNase PH]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17576666 PubMed]
  
 
=Biological materials =
 
=Biological materials =
Line 128: Line 100:
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
−
* '''GFP fusion:'''
+
=Labs working on this gene/protein=
−
 
 
−
* '''two-hybrid system:'''
 
  
−
* '''Antibody:'''
+
[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]
−
 
 
−
=Labs working on this gene/protein=
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 140: Line 108:
 
=References=
 
=References=
  
−
<pubmed>19087206, 12110595, 16415880 </pubmed>
+
<pubmed>9346318,2468993,17576666, 1372600,7506707 1383945 7538759 10224127 9677377 8662730 10222262</pubmed>
  
−
[[Category:Protein-coding genes]]
+
[[Category:small RNA]]

Revision as of 14:54, 11 November 2013

  • Description: 4.5 S RNA

Gene name scr
Synonyms
Essential yes
Product small cytoplasmic RNA (scRNA, 4.5S RNA),

signal recognition particle-like (SRP) component

Function presecretory protein translocation
Interactions involving this RNA in SubtInteract: Scr
Immediate neighbours yaaJ, dnaX
Gene sequence (+200bp) Protein sequence
Genetic context
Scr context.gif
This image was kindly provided by SubtiList







Categories containing this gene/protein

protein secretion, essential genes, ncRNA

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag:

Phenotypes of a mutant

  • the gene is essential PubMed

Database entries

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

Additional information

The RNA

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:

Extended information on the RNA

  • Kinetic information

Database entries

  • Structure:

Additional information

Expression and regulation

  • Sigma factor: SigA (both promoters)
  • Regulation:
  • Regulatory mechanism:
  • Additional information: transcribed as 354 nt precursor, cleaved at the 5' end by RNase III and at the 3' site by RNase J1 to yield a 275 nt molecule, final trimming to 271 nt sc RNA by RNase PH PubMed

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:

Labs working on this gene/protein

David Bechhofer, Mount Sinai School, New York, USA Homepage

Your additional remarks

References

Shiyi Yao, Joshua B Blaustein, David H Bechhofer
Processing of Bacillus subtilis small cytoplasmic RNA: evidence for an additional endonuclease cleavage site.
Nucleic Acids Res: 2007, 35(13);4464-73
[PubMed:17576666] [WorldCat.org] [DOI] (I p)

K Nakamura, S Yahagi, T Yamazaki, K Yamane
Bacillus subtilis histone-like protein, HBsu, is an integral component of a SRP-like particle that can bind the Alu domain of small cytoplasmic RNA.
J Biol Chem: 1999, 274(19);13569-76
[PubMed:10224127] [WorldCat.org] [DOI] (P p)

T Yamazaki, S Yahagi, K Nakamura, K Yamane
Depletion of Bacillus subtilis histone-like protein, HBsu, causes defective protein translocation and induces upregulation of small cytoplasmic RNA.
Biochem Biophys Res Commun: 1999, 258(1);211-4
[PubMed:10222262] [WorldCat.org] [DOI] (P p)

A Oguro, H Kakeshita, K Nakamura, K Yamane, W Wang, D H Bechhofer
Bacillus subtilis RNase III cleaves both 5'- and 3'-sites of the small cytoplasmic RNA precursor.
J Biol Chem: 1998, 273(31);19542-7
[PubMed:9677377] [WorldCat.org] [DOI] (P p)

H Takamatsu, K Bunai, T Horinaka, A Oguro, K Nakamura, K Watabe, K Yamane
Identification of a region required for binding to presecretory protein in Bacillus subtilis Ffh, a homologue of the 54-kDa subunit of mammalian signal recognition particle.
Eur J Biochem: 1997, 248(2);575-82
[PubMed:9346318] [WorldCat.org] [DOI] (P p)

K Kurita, K Honda, S Suzuma, H Takamatsu, K Nakamura, K Yamane
Identification of a region of Bacillus subtilis Ffh, a homologue of mammalian SRP54 protein, that is essential for binding to small cytoplasmic RNA.
J Biol Chem: 1996, 271(22);13140-6
[PubMed:8662730] [WorldCat.org] [DOI] (P p)

T Shibata, Y Nakamura, K Nakamura, K Yamane
Depletion of small cytoplasmic RNA confers fusidic-acid resistance on Bacillus subtilis.
Biochem Biophys Res Commun: 1995, 210(2);317-23
[PubMed:7538759] [WorldCat.org] [DOI] (P p)

M Nishiguchi, K Honda, R Amikura, K Nakamura, K Yamane
Structural requirements of Bacillus subtilis small cytoplasmic RNA for cell growth, sporulation, and extracellular enzyme production.
J Bacteriol: 1994, 176(1);157-65
[PubMed:7506707] [WorldCat.org] [DOI] (P p)

K Nakamura, M Minemura, M Nishiguchi, K Honda, A Nakamura, K Yamane
Conserved residues and secondary structure found in small cytoplasmic RNAs from thirteen Bacillus species.
Nucleic Acids Res: 1992, 20(19);5227-8
[PubMed:1383945] [WorldCat.org] [DOI] (P p)

K Nakamura, Y Imai, A Nakamura, K Yamane
Small cytoplasmic RNA of Bacillus subtilis: functional relationship with human signal recognition particle 7S RNA and Escherichia coli 4.5S RNA.
J Bacteriol: 1992, 174(7);2185-92
[PubMed:1372600] [WorldCat.org] [DOI] (P p)

J C Struck, R K Hartmann, H Y Toschka, V A Erdmann
Transcription and processing of Bacillus subtilis small cytoplasmic RNA.
Mol Gen Genet: 1989, 215(3);478-82
[PubMed:2468993] [WorldCat.org] [DOI] (P p)

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