Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
 
(154 intermediate revisions by 5 users not shown)
Line 1: Line 1:
−
* '''Description:''' replication initiation protein <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
−
|''dnaA''
+
|''glmS''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaH, dnaJ, dnaK ''
+
|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''' || replication initiation protein
+
|style="background:#ABCDEF;" align="center"| '''Product''' || glutamine-fructose-6-phosphate transaminase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || [[DNA replication]]
+
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/dnaA/ DnaA]
+
|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"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/DnaA DnaA]
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 65 kDa, 4.796 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 6.035 
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1800 bp, 600 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1338 bp, 446 aa
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glmM]]'', ''[[ybbU]]''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rpmH]]'', ''[[dnaN]]''
+
|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)'''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11777&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|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>
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:DnaA_dnaN_yaaA_recF_yaaB_gyrB_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=dnaA_410_1750_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:dnaA_expression.png|500px]]
+
|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]]
 
|-
 
|-
 
|}
 
|}
Line 44: Line 46:
  
 
= [[Categories]] containing this gene/protein =
 
= [[Categories]] containing this gene/protein =
−
{{SubtiWiki category|[[DNA replication]]}},
+
{{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|[[Spo0A regulon]]}}
+
{{SubtiWiki regulon|[[glmS ribozyme]]}}
−
=The [[DnaA regulon]]=
+
 
 
=The gene=
 
=The gene=
  
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00010
+
* '''Locus tag:''' BSU01780
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 61: 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/dnaAN.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10065]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10948]
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=The protein=
 
=The protein=
Line 73: Line 77:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' L-glutamine + D-fructose 6-phosphate = L-glutamate + D-glucosamine 6-phosphate (according to Swiss-Prot)
  
−
* '''Protein family:''' dnaA family (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 83: Line 87:
 
* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:''' AAA+ domain
+
* '''Domains:'''  
  
 
* '''Modification:'''
 
* '''Modification:'''
Line 90: Line 94:
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
−
** [[SirA]] displaces [[DnaA]] from the replication origin {{PubMed|19682252}}
 
−
** [[YabA]] inhibits co-operative binding of DnaA to the ''oriC'' DNA {{PubMed|21895792}}
 
−
** DnaA helix formation (and thus replication initiation) is inhibited by the interaction of [[Soj]] with the AAA+ domain of DnaA {{PubMed|22286949}}
 
  
 
* '''[[SubtInteract|Interactions]]:'''
 
* '''[[SubtInteract|Interactions]]:'''
−
** [[DnaA]] assembles into a right-handed helical oligomer built upon interactions between neighbouring AAA+ domains
 
−
** [[Soj]]-[[DnaA]] {{PubMed|22286949}}
 
−
** [[DnaA]]-[[YabA]],  [[DnaA]]-[[YabA]]-[[DnaN]] {{PubMed|12060778}}
 
−
** [[DnaA]]-[[DnaD]] [http://www.ncbi.nlm.nih.gov/sites/entrez/11222620 PubMed]
 
−
** [[SirA]]-[[DnaA]] {{PubMed|19682252,21239581}}
 
−
** [[YqaH]]-[[DnaA]] {{PubMed|12060778}}
 
  
−
* '''[[Localization]]:''' throughout the cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/10844689 PubMed]
+
* '''[[Localization]]:'''
 +
** cytoplasm (according to Swiss-Prot)
  
 
=== 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.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/P05648 P05648]
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P39754 P39754]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00010]
+
* '''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 [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:''' ''[[dnaA]]-[[dnaN]]'' [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=dnaA_410_1750_1 dnaA] {{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:''' negatively controlled by [[DnaA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2168872 PubMed] and [[Spo0A]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
+
* '''Regulation:'''  
−
** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
+
** 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
−
** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
 
  
−
* '''Additional information:'''
+
* '''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 147: Line 153:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
[[Philippe Noirot]], Jouy-en-Josas, France [http://locus.jouy.inra.fr/cms/index.php?id=18 homepage]
 
  
−
[[Peter Graumann]], Freiburg University, Germany [http://www.biologie.uni-freiburg.de/data/bio2/graumann/index.htm homepage]
+
[[Wade Winkler]], University of Texas, USA, [http://www.utsouthwestern.edu/findfac/professional/0,,68018,00.html Homepage]
−
 
 
−
[[Alan Grossman]], MIT, Cambridge, MA, USA
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 157: Line 160:
 
=References=
 
=References=
 
==Reviews==
 
==Reviews==
−
<pubmed> 20157337 21035377 21639790</pubmed>
+
<pubmed> 18279655 </pubmed>
−
==The [[DnaA regulon]]==
+
 
−
<pubmed> 16120674, </pubmed>
+
==The ''glmS'' Ribozyme==
−
==Original publications==
+
<pubmed>18079181 ,16484375, 16784238 ,15096624 , 16990543 ,17114942 ,16484375 , 15029187, 17283212 , 16298301, 19228039 21317896 21395279 </pubmed>
−
'''Additional publications:''' {{PubMed|22396664,21911367}}
 
−
<pubmed>18854156,19011033, 11222620,14651647,17140409 10844689 ,11222620 12060778 16461910 2987848 2168872 11207367, 19737352 19081080 17932079 19968790 19682252 20511500 21097613 21239581 21895792 22286949</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


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

Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=206021"