Difference between revisions of "RibU"
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| − | * '''Description:''' riboflavin transporter <br/><br/> | + | * '''Description:''' riboflavin [[ECF transporter]], S protein <br/><br/> |
{| align="right" border="1" cellpadding="2" | {| align="right" border="1" cellpadding="2" | ||
| Line 10: | Line 10: | ||
|style="background:#ABCDEF;" align="center"| '''Essential''' || no | |style="background:#ABCDEF;" align="center"| '''Essential''' || no | ||
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''Product''' || riboflavin transporter | + | |style="background:#ABCDEF;" align="center"| '''Product''' || S protein of riboflavin [[ECF transporter]] |
|- | |- | ||
|style="background:#ABCDEF;" align="center"|'''Function''' || riboflavin uptake | |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 | ||
| Line 20: | Line 26: | ||
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fer]]'', ''[[ypzE]]'' | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fer]]'', ''[[ypzE]]'' | ||
|- | |- | ||
| − | | | + | |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] |
|- | |- | ||
|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> | <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]'''   {{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/> | ||
| + | |||
| + | = [[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= | ||
| Line 40: | Line 58: | ||
=== Database entries === | === Database entries === | ||
| + | * '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU23050&redirect=T BSU23050] | ||
* '''DBTBS entry:''' no entry | * '''DBTBS entry:''' no entry | ||
| Line 46: | Line 65: | ||
=== Additional information=== | === Additional information=== | ||
| − | |||
=The protein= | =The protein= | ||
| Line 62: | Line 80: | ||
* '''Kinetic information:''' | * '''Kinetic information:''' | ||
| − | * '''Domains:''' | + | * '''[[Domains]]:''' |
* '''Modification:''' | * '''Modification:''' | ||
| − | * ''' | + | * '''[[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'') |
* '''UniProt:''' [http://www.uniprot.org/uniprot/P50726 P50726] | * '''UniProt:''' [http://www.uniprot.org/uniprot/P50726 P50726] | ||
| Line 88: | Line 108: | ||
=Expression and regulation= | =Expression and regulation= | ||
| − | * '''Operon:''' there is a promoter directly in front of ''ribU'' {{PubMed|17693491}} | + | * '''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}} | ||
* '''[[Sigma factor]]:''' | * '''[[Sigma factor]]:''' | ||
| Line 97: | Line 120: | ||
* '''Additional information:''' | * '''Additional information:''' | ||
| + | ** the mRNA is substantially stabilized upon depletion of [[Rny|RNase Y]] {{PubMed|21815947}} | ||
=Biological materials = | =Biological materials = | ||
| Line 117: | Line 141: | ||
=References= | =References= | ||
| − | + | ==Reviews== | |
| − | <pubmed>12456892,,17693491, </pubmed> | + | <pubmed> 20497229 22574898 24362466 </pubmed> |
| + | ==Original publications== | ||
| + | <pubmed>12456892, 20972419,17693491,21815947 24356467 24755604 25438558 </pubmed> | ||
[[Category:Protein-coding genes]] | [[Category:Protein-coding genes]] | ||
Latest revision as of 18:10, 5 December 2014
- Description: riboflavin ECF transporter, S protein
| 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 
This image was kindly provided by SubtiList
| |
| Expression at a glance PubMed 500px | |
Contents
Categories containing this gene/protein
ECF transporter, biosynthesis of cofactors, membrane proteins
This gene is a member of the following regulons
The gene
Basic information
- Locus tag: BSU23050
Phenotypes of a mutant
Database entries
- BsubCyc: BSU23050
- 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:
- Localization: membrane
Database entries
- BsubCyc: BSU23050
- Structure: 3P5N (RibU from Staphylococcus aureus)
- UniProt: P50726
- KEGG entry: [2]
- E.C. number:
Additional information
Expression and regulation
- Regulatory mechanism: FMN-box: riboswitch, controls access of the ribosome to the Shine-Dalgarno sequence 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)
