Difference between revisions of "RibU"

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m (YpaA moved to RibU)
 
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* '''Description:''' write here <br/><br/>
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* '''Description:''' riboflavin [[ECF transporter]], S protein <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'''
−
|''ypaA''
+
|''ribU ''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ribU ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ypaA''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' ||  
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' ||  
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|style="background:#ABCDEF;" align="center"| '''Product''' || S protein of riboflavin [[ECF transporter]]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
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|style="background:#ABCDEF;" align="center"|'''Function''' || riboflavin uptake
 +
|-
 +
|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=BSU23050 ribU]
 +
|-
 +
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=RibU RibU]
 +
|-
 +
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=ribU ribU]'''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 20 kDa, 10.12   
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 20 kDa, 10.12   
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 570 bp, 190 aa  
 
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 570 bp, 190 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||  
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fer]]'', ''[[ypzE]]''
 
|-
 
|-
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ypaA_nucleotide.txt    Gene sequence     (+200bp)  ]'''
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|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU23050 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU23050 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU23050 DNA_with_flanks]
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ypaA_protein.txt Protein sequence]'''
 
 
|-
 
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ypaA_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ypaA_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=fmnP_2410017_2410589_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ribU_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU23050]]
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/>
  
−
<br/><br/>
+
= [[Categories]] containing this gene/protein =
 +
{{SubtiWiki category|[[ECF transporter]]}},
 +
{{SubtiWiki category|[[biosynthesis of cofactors]]}},
 +
{{SubtiWiki category|[[membrane proteins]]}}
 +
 
 +
= This gene is a member of the following [[regulons]] =
 +
{{SubtiWiki regulon|[[FMN-box]]}}
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Locus tag:''' BSU23050
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU23050&redirect=T BSU23050]
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ypaA.html]
+
* '''DBTBS entry:''' no entry
  
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11428]
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11428]
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=The protein=
 
=The protein=
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* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:'''  
+
* '''[[Domains]]:'''  
  
 
* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):'''
+
* '''[[Cofactors]]:'''
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''[[SubtInteract|Interactions]]:'''
 +
** [[YbaF]]-[[RibU]] {{PubMed|20497229}}
  
−
* '''Localization:'''
+
* '''[[Localization]]:''' membrane
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU23050&redirect=T BSU23050]
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3P5N 3P5N] (RibU from ''Staphylococcus aureus'')
  
−
* '''Swiss prot entry:'''
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* '''UniProt:''' [http://www.uniprot.org/uniprot/P50726 P50726]
  
−
* '''KEGG entry:'''
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* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23050]
  
 
* '''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:''' ''[[ribU]]'' {{PubMed|21815947}}
 +
** there is a promoter directly in front of ''[[ribU]]'' {{PubMed|17693491}}
 +
 
 +
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fmnP_2410017_2410589_-1 ribU] {{PubMed|22383849}}
  
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* '''Sigma factor:'''  
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* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
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* '''Regulation:''' expressed in the absence of FMN ([[FMN-box]]) {{PubMed|17693491}}
  
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* '''Regulatory mechanism:'''  
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* '''Regulatory mechanism:''' [[FMN-box]]: [[riboswitch]], controls access of the ribosome to the Shine-Dalgarno sequence {{PubMed|12456892}}
  
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* '''Additional information:'''  
+
* '''Additional information:'''
 +
** the mRNA is substantially stabilized upon depletion of [[Rny|RNase Y]] {{PubMed|21815947}}
  
 
=Biological materials =
 
=Biological materials =
  
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* '''Mutant:'''
+
* '''Mutant:'''  
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
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=References=
 
=References=
 +
==Reviews==
 +
<pubmed> 20497229 22574898 24362466 </pubmed>
 +
==Original publications==
 +
<pubmed>12456892, 20972419,17693491,21815947  24356467 24755604 25438558 </pubmed>
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
[[Category:Protein-coding genes]]

Latest revision as of 18:10, 5 December 2014

Gene name ribU
Synonyms ypaA
Essential no
Product S protein of riboflavin ECF transporter
Function riboflavin uptake
Gene expression levels in SubtiExpress: ribU
Interactions involving this protein in SubtInteract: RibU
Metabolic function and regulation of this protein in SubtiPathways:
ribU
MW, pI 20 kDa, 10.12
Gene length, protein length 570 bp, 190 aa
Immediate neighbours fer, ypzE
Sequences Protein DNA DNA_with_flanks
Genetic context
YpaA context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
500px















Categories containing this gene/protein

ECF transporter, biosynthesis of cofactors, membrane proteins

This gene is a member of the following regulons

FMN-box

The gene

Basic information

  • Locus tag: BSU23050

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:
  • Modification:
  • Effectors of protein activity:

Database entries

  • Structure: 3P5N (RibU from Staphylococcus aureus)
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Additional information:
    • the mRNA is substantially stabilized upon depletion of RNase Y PubMed

Biological materials

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

Labs working on this gene/protein

Your additional remarks

References

Reviews

Dirk J Slotboom
Structural and mechanistic insights into prokaryotic energy-coupling factor transporters.
Nat Rev Microbiol: 2014, 12(2);79-87
[PubMed:24362466] [WorldCat.org] [DOI] (I p)

Guus B Erkens, Maria Majsnerowska, Josy ter Beek, Dirk Jan Slotboom
Energy coupling factor-type ABC transporters for vitamin uptake in prokaryotes.
Biochemistry: 2012, 51(22);4390-6
[PubMed:22574898] [WorldCat.org] [DOI] (I p)

Thomas Eitinger, Dmitry A Rodionov, Mathias Grote, Erwin Schneider
Canonical and ECF-type ATP-binding cassette importers in prokaryotes: diversity in modular organization and cellular functions.
FEMS Microbiol Rev: 2011, 35(1);3-67
[PubMed:20497229] [WorldCat.org] [DOI] (I p)

Original publications

S A Sklyarova, A S Mironov
[Bacillus subtilis ypaA gene regulation mechanism involves FMN-binding sensor RNA].
Genetika: 2014, 50(3);364-8
[PubMed:25438558] [WorldCat.org] (P p)

Jennifer Frommer, Robert Hieronymus, Tamil Selvi Arunachalam, Sabine Heeren, Maria Jenckel, Anne Strahl, Bettina Appel, Sabine Müller
Preparation of modified long-mer RNAs and analysis of FMN binding to the ypaA aptamer from B. subtilis.
RNA Biol: 2014, 11(5);609-23
[PubMed:24755604] [WorldCat.org] [DOI] (I p)

Jianing Song, Changge Ji, John Z H Zhang
Unveiling the gating mechanism of ECF transporter RibU.
Sci Rep: 2013, 3;3566
[PubMed:24356467] [WorldCat.org] [DOI] (I e)

Martin Lehnik-Habrink, Marc Schaffer, Ulrike Mäder, Christine Diethmaier, Christina Herzberg, Jörg Stülke
RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y.
Mol Microbiol: 2011, 81(6);1459-73
[PubMed:21815947] [WorldCat.org] [DOI] (I p)

Peng Zhang, Jiawei Wang, Yigong Shi
Structure and mechanism of the S component of a bacterial ECF transporter.
Nature: 2010, 468(7324);717-20
[PubMed:20972419] [WorldCat.org] [DOI] (I p)

Christian Vogl, Simon Grill, Oliver Schilling, Jörg Stülke, Matthias Mack, Jürgen Stolz
Characterization of riboflavin (vitamin B2) transport proteins from Bacillus subtilis and Corynebacterium glutamicum.
J Bacteriol: 2007, 189(20);7367-75
[PubMed:17693491] [WorldCat.org] [DOI] (P p)

Wade C Winkler, Smadar Cohen-Chalamish, Ronald R Breaker
An mRNA structure that controls gene expression by binding FMN.
Proc Natl Acad Sci U S A: 2002, 99(25);15908-13
[PubMed:12456892] [WorldCat.org] [DOI] (P p)

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