Difference between revisions of "Sandbox"

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−
* '''Description:''' DNA gyrase (subunit A) <br/><br/>
+
* '''Description:''' glutamine-fructose-6-phosphate transaminase <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''' glaube ich oder nicht
−
|''gyrA''
+
|''glmS''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''nalA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''gcaA, ybxD ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA gyrase (subunit A)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || glutamine-fructose-6-phosphate transaminase
 +
|-
 +
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || DNA supercoiling, <br/>initation of replication cycle and DNA elongation
+
|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=sandbox sandbox]'''
 
|-
 
|-
−
|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=BSU00070 GyrA]
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 65 kDa, 4.796 
 
|-
 
|-
−
|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=GyrA GyrA]
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1800 bp, 600 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 91 kDa, 5.215 
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glmM]]'', ''[[ybbU]]''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2463 bp, 821 aa
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11954&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gyrB]]'', ''[[rrnO-16S]]''
+
|colspan="2" | '''Genetic context''' <br/> [[Image:quintos.gif]]
 +
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00070 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00070 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00070 DNA_with_flanks]
 
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:GyrA_context.png]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:test.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=gyrA_6994_9459_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:gyrA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00070]]
+
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=glmS_200277_202079_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:glmS_expression.png|500px]]
 
|-
 
|-
 
|}
 
|}
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<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|[[DNA condensation/ segregation]]}},
+
{{SubtiWiki category|[[cell wall synthesis]]}},
 +
{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
 
{{SubtiWiki category|[[essential genes]]}}
 
{{SubtiWiki category|[[essential genes]]}}
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
−
 
+
{{SubtiWiki regulon|[[glmS ribozyme]]}}
  
 
=The gene=
 
=The gene=
Line 49: Line 57:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00070
+
* '''Locus tag:''' BSU01780
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 56: Line 64:
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [HELLO BSU00100]
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00240&redirect=T"]
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gyrA.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10071]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10948]
  
 
=== Additional information===
 
=== Additional information===
−
 
−
 
−
 
  
 
=The protein=
 
=The protein=
Line 70: Line 77:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' ATP-dependent breakage, passage and rejoining of double-stranded DNA (according to Swiss-Prot)  
+
* '''Catalyzed reaction/ biological activity:''' L-glutamine + D-fructose 6-phosphate = L-glutamate + D-glucosamine 6-phosphate (according to Swiss-Prot)  
  
−
* '''Protein family:''' topoisomerase gyrA/parC subunit family (according to Swiss-Prot)
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[ParC]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 89: Line 96:
  
 
* '''[[SubtInteract|Interactions]]:'''
 
* '''[[SubtInteract|Interactions]]:'''
−
** [[GyrA]]-[[GyrB]]
 
  
−
* '''[[Localization]]:'''  
+
* '''[[Localization]]:'''
−
** Nucleoid (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
+
** cytoplasm (according to Swiss-Prot)
−
** nucleoid-associated in actively growing cells [http://www.ncbi.nlm.nih.gov/sites/entrez/9539793 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [HELLO BSU00100]
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00240&redirect=T BSU00240]
  
−
* '''Structure:'''
+
* '''Structure:'''
−
** [http://www.rcsb.org/pdb/explore/explore.do?structureId=4DDQ 4DDQ] (DNA gyrase A-subunit lacking the C-terminal DNA-wrapping domains) {{PubMed|23602808}}
+
**[http://www.pdb.org/pdb/explore/explore.do?structureId=HIV2 HIV2] (from ''Bacillus subtilis'', 100% identity) {{PubMed|13454352}}
 +
** [http://www.pdb.org/pdb/explore/explore.do?structureId=2VF4 2VF4] (GlmS from ''E. coli'', 39% identity, 58% similarity) {{PubMed|18295797}}
 +
** the ribozyme: [http://www.rcsb.org/pdb/explore.do?structureId=3g8s 3G8S], [http://www.rcsb.org/pdb/explore.do?structureId=3G9C 3G9C], [http://www.rcsb.org/pdb/explore.do?structureId=3g8t 3G8T], [http://www.rcsb.org/pdb/explore.do?structureId=3g95 3G95], [http://www.rcsb.org/pdb/explore.do?structureId=3g96 3G96] (all for the ribozyme from ''Bacillus anthracis''), [http://www.rcsb.org/pdb/explore.do?structureId=2HO7 2HO7] (the ribozyme from ''Thermonanaerobacter tengcongensis'')
  
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/P05653 P05653]
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P39754 P39754]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00070]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01780]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.6.1.16 2.6.1.16]
  
 
=== Additional information===
 
=== Additional information===
  
−
:* subject to Clp-dependent proteolysis upon glucose starvation {{PubMed|17981983}}
+
:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
−
 
 
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''gyrA'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
* '''Operon:''' ''[[ybbP]]-[[ybbR]]-[[glmM]]-[[glmS]]''
  
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gyrA_6994_9459_1 gyrA] {{PubMed|22383849}}
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=glmS_200277_202079_1 glmS] {{PubMed|22383849}}
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
* '''Sigma factor:''' [[SigA]] {{PubMed|22211522}}
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
 +
** repressed by glucosamine, N-acetylglucosamine, N-propionylglucosamine or N-formylglucosamine {{PubMed|14343123}}
 +
** ''glmS'' is only expressed in the absence of glucosamine 6-phosphate ([[glmS]] [[ribozyme]])
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' ''glmS'' [[ribozyme]]: glucosamine 6-phosphate binds the leader mRNA, and a [[riboswitch]] with [[ribozyme]] activity cleaves off the ''[[glmS]]'' section from the mRNA, resulting in stopp of transcript elongation
  
−
* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed],  GyrA is subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
+
* '''Additional information:'''  
 +
** subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 +
** A [[ncRNA]] is predicted between ''[[glmM]]'' and ''[[glmS]]'' {{PubMed|20525796}}
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium): 2000 {{PubMed|24696501}}
 +
** number of protein molecules per cell (complex medium with amino acids, without glucose): 4000 {{PubMed|24696501}}
  
 
=Biological materials =
 
=Biological materials =
Line 140: Line 154:
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
  
−
[[Dagmar Klostermeier]], Biozentrum Basel, Switzerland [http://www.biozentrum.unibas.ch/klostermeier/index.html homepage]
+
[[Wade Winkler]], University of Texas, USA, [http://www.utsouthwestern.edu/findfac/professional/0,,68018,00.html Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
  
 
=References=
 
=References=
−
<pubmed>16479537,17981983 ,9539793 , 2987848  19666507 17320901 23475963 23602808 20870749</pubmed>
+
==Reviews==
 +
<pubmed> 18279655 </pubmed>
 +
 
 +
==The ''glmS'' Ribozyme==
 +
<pubmed>18079181 ,16484375, 16784238 ,15096624 , 16990543 ,17114942 ,16484375 , 15029187, 17283212 , 16298301, 19228039 21317896 21395279 </pubmed>
  
 +
==Other Original Publications==
 +
'''Additional publications:''' {{PubMed|22211522}}
 +
<pubmed> 14343123 17981983 ,11160890, 18295797 20525796  </pubmed>
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Latest revision as of 13:22, 29 July 2014

  • Description: glutamine-fructose-6-phosphate transaminase

Gene name glaube ich oder nicht glmS
Synonyms gcaA, ybxD
Essential yes PubMed
Product glutamine-fructose-6-phosphate transaminase
Function cell wall synthesis
Metabolic function and regulation of this protein in SubtiPathways:
sandbox
MW, pI 65 kDa, 4.796
Gene length, protein length 1800 bp, 600 aa
Immediate neighbours glmM, ybbU
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
File:Quintos.gif
This image was kindly provided by SubtiList
Genetic context
Test.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
GlmS expression.png
























Categories containing this gene/protein

cell wall synthesis, biosynthesis of cell wall components, essential genes

This gene is a member of the following regulons

glmS ribozyme

The gene

Basic information

  • Locus tag: BSU01780

Phenotypes of a mutant

essential PubMed

Database entries

  • BsubCyc: [HELLO BSU00100]
  • BsubCyc: "
  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: L-glutamine + D-fructose 6-phosphate = L-glutamate + D-glucosamine 6-phosphate (according to Swiss-Prot)
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • BsubCyc: [HELLO BSU00100]
  • BsubCyc: BSU00240
  • Structure:
    • HIV2 (from Bacillus subtilis, 100% identity) PubMed
    • 2VF4 (GlmS from E. coli, 39% identity, 58% similarity) PubMed
    • the ribozyme: 3G8S, 3G9C, 3G8T, 3G95, 3G96 (all for the ribozyme from Bacillus anthracis), 2HO7 (the ribozyme from Thermonanaerobacter tengcongensis)
  • KEGG entry: [2]

Additional information

  • subject to Clp-dependent proteolysis upon glucose starvation PubMed

Expression and regulation

  • Regulation:
    • repressed by glucosamine, N-acetylglucosamine, N-propionylglucosamine or N-formylglucosamine PubMed
    • glmS is only expressed in the absence of glucosamine 6-phosphate (glmS ribozyme)
  • Regulatory mechanism: glmS ribozyme: glucosamine 6-phosphate binds the leader mRNA, and a riboswitch with ribozyme activity cleaves off the glmS section from the mRNA, resulting in stopp of transcript elongation
  • Additional information:
    • subject to Clp-dependent proteolysis upon glucose starvation PubMed
    • A ncRNA is predicted between glmM and glmS PubMed
    • number of protein molecules per cell (minimal medium with glucose and ammonium): 2000 PubMed
    • number of protein molecules per cell (complex medium with amino acids, without glucose): 4000 PubMed

Biological materials

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

Labs working on this gene/protein

Wade Winkler, University of Texas, USA, Homepage

Your additional remarks

References

Reviews

Philippe Durand, Béatrice Golinelli-Pimpaneau, Stéphane Mouilleron, Bernard Badet, Marie-Ange Badet-Denisot
Highlights of glucosamine-6P synthase catalysis.
Arch Biochem Biophys: 2008, 474(2);302-17
[PubMed:18279655] [WorldCat.org] [DOI] (I p)


The glmS Ribozyme

Krista M Brooks, Ken J Hampel
Rapid steps in the glmS ribozyme catalytic pathway: cation and ligand requirements.
Biochemistry: 2011, 50(13);2424-33
[PubMed:21395279] [WorldCat.org] [DOI] (I p)

Peter Y Watson, Martha J Fedor
The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo.
Nat Struct Mol Biol: 2011, 18(3);359-63
[PubMed:21317896] [WorldCat.org] [DOI] (I p)

Jesse C Cochrane, Sarah V Lipchock, Kathryn D Smith, Scott A Strobel
Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme.
Biochemistry: 2009, 48(15);3239-46
[PubMed:19228039] [WorldCat.org] [DOI] (I p)

Jennifer A Collins, Irnov Irnov, Stephanie Baker, Wade C Winkler
Mechanism of mRNA destabilization by the glmS ribozyme.
Genes Dev: 2007, 21(24);3356-68
[PubMed:18079181] [WorldCat.org] [DOI] (P p)

Rebecca A Tinsley, Jennifer R W Furchak, Nils G Walter
Trans-acting glmS catalytic riboswitch: locked and loaded.
RNA: 2007, 13(4);468-77
[PubMed:17283212] [WorldCat.org] [DOI] (P p)

Kenneth Blount, Izabela Puskarz, Robert Penchovsky, Ronald Breaker
Development and application of a high-throughput assay for glmS riboswitch activators.
RNA Biol: 2006, 3(2);77-81
[PubMed:17114942] [WorldCat.org] [DOI] (I p)

Daniel J Klein, Adrian R Ferré-D'Amaré
Structural basis of glmS ribozyme activation by glucosamine-6-phosphate.
Science: 2006, 313(5794);1752-6
[PubMed:16990543] [WorldCat.org] [DOI] (I p)

Ken J Hampel, Melissa M Tinsley
Evidence for preorganization of the glmS ribozyme ligand binding pocket.
Biochemistry: 2006, 45(25);7861-71
[PubMed:16784238] [WorldCat.org] [DOI] (P p)

Adam Roth, Ali Nahvi, Mark Lee, Inbal Jona, Ronald R Breaker
Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions.
RNA: 2006, 12(4);607-19
[PubMed:16484375] [WorldCat.org] [DOI] (P p)

Tom J McCarthy, Melissa A Plog, Shennen A Floy, Joshua A Jansen, Juliane K Soukup, Garrett A Soukup
Ligand requirements for glmS ribozyme self-cleavage.
Chem Biol: 2005, 12(11);1221-6
[PubMed:16298301] [WorldCat.org] [DOI] (P p)

Jeffrey E Barrick, Keith A Corbino, Wade C Winkler, Ali Nahvi, Maumita Mandal, Jennifer Collins, Mark Lee, Adam Roth, Narasimhan Sudarsan, Inbal Jona, J Kenneth Wickiser, Ronald R Breaker
New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control.
Proc Natl Acad Sci U S A: 2004, 101(17);6421-6
[PubMed:15096624] [WorldCat.org] [DOI] (P p)

Wade C Winkler, Ali Nahvi, Adam Roth, Jennifer A Collins, Ronald R Breaker
Control of gene expression by a natural metabolite-responsive ribozyme.
Nature: 2004, 428(6980);281-6
[PubMed:15029187] [WorldCat.org] [DOI] (I p)


Other Original Publications

Additional publications: PubMed

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