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 This image was kindly provided by SubtiList
Expression at a glance PubMed

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:

Interactions:

Localization:
- cytoplasm (according to Swiss-Prot)

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)

UniProt: P39754

KEGG entry: [2]

E.C. number: 2.6.1.16

Additional information

subject to Clp-dependent proteolysis upon glucose starvation PubMed

Expression and regulation

Operon: ybbP-ybbR-glmM-glmS

Expression browser: glmS PubMed

Sigma factor: SigA PubMed

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

@@ Line 1: / Line 1: @@
-* '''Description:''' ATP-dependent Clp protease ATP-binding subunit (class III heat-shock protein) <br/><br/>
+* '''Description:''' glutamine-fructose-6-phosphate transaminase <br/><br/>
 {| align="right" border="1" cellpadding="2"
 |-
-|style="background:#ABCDEF;" align="center"|'''Gene name'''
+|style="background:#ABCDEF;" align="center"|'''Gene name''' glaube ich oder nicht
-|''clpX''
+|''glmS''
 |-
-|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''gcaA, ybxD ''
 |-
-|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || ATP-dependent Clp protease ATP-binding subunit
+|style="background:#ABCDEF;" align="center"| '''Product''' || glutamine-fructose-6-phosphate transaminase
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
+|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress]'''
+|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]'''
 |-
-|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 4.645
+|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 65 kDa, 4.796
 |-
-|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1260 bp, 420 aa
+|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1800 bp, 600 aa
 |-
-|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lonB]]'', ''[[tig]]''
+|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glmM]]'', ''[[ybbU]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14782&#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:CAB11954&#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:clpX_context.gif]]
+|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>
+|-
+|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]]
 |-
 |}
 __TOC__
+<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 =
+{{SubtiWiki category|[[cell wall synthesis]]}},
+{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
+{{SubtiWiki category|[[essential genes]]}}
+= This gene is a member of the following [[regulons]] =
+{{SubtiWiki regulon|[[glmS ribozyme]]}}
 =The gene=
@@ Line 39: / Line 57: @@
 === Basic information ===
-* '''Locus tag:''' BSU28220
+* '''Locus tag:''' BSU01780
 ===Phenotypes of a mutant ===
+essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 === 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/clpX.html]
+* '''DBTBS entry:''' no entry
-* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11387]
+* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10948]
 === Additional information===
 =The protein=
@@ Line 56: / Line 77: @@
 === Basic information/ Evolution ===
-* '''Catalyzed reaction/ biological activity:''' ATPase/chaperone
+* '''Catalyzed reaction/ biological activity:''' L-glutamine + D-fructose 6-phosphate = L-glutamate + D-glucosamine 6-phosphate (according to Swiss-Prot)
-* '''Protein family:''' clpX chaperone family (according to Swiss-Prot) ClpX (IP004487) [http://www.ebi.ac.uk/interpro/IEntry?ac=IPR004487 InterPro], AAA+ -type ATPase (IPR013093) [http://www.ebi.ac.uk/interpro/IEntry?ac=IPR013093 InterPro] (PF07724) [http://pfam.sanger.ac.uk/family?acc=PF07724 PFAM]
+* '''Protein family:'''
-* '''Paralogous protein(s):''' [[ClpC]], [[ClpE]]
+* '''Paralogous protein(s):'''
 === Extended information on the protein ===
@@ Line 66: / Line 87: @@
 * '''Kinetic information:'''
-* '''Domains:''' AAA-ATPase [http://pfam.sanger.ac.uk/family?acc=PF07724 PFAM], Zinc finger [http://pfam.sanger.ac.uk/family?acc=PF06689 PFAM]
+* '''Domains:'''
 * '''Modification:'''
@@ Line 74: / Line 95: @@
 * '''Effectors of protein activity:'''
-* '''Interactions:''' [[ClpP]]-[[ClpX]]
+* '''[[SubtInteract|Interactions]]:'''
-* '''Localization:''' cytoplasmic polar clusters, excluded from the nucleoid, induced clustering upon heatshock, colocalization with [[ClpP]] [http://www.ncbi.nlm.nih.gov/pubmed/18786145 Pubmed]
+* '''[[Localization]]:'''
-[[File:ClpX.jpg‎ ]]
+** cytoplasm (according to Swiss-Prot)
 === Database entries ===
+* '''BsubCyc:''' [HELLO BSU00100]
+* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00240&redirect=T BSU00240]
-* '''Structure:''' homologue structure resolved [http://www.rcsb.org/pdb/explore/explore.do?structureId=1UM8 1UM8], structural model of ''B. subtilis'' ClpX available from [http://subtiwiki.uni-goettingen.de/wiki/index.php/User:Hstrahl hstrahl]
+* '''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'')
-* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P50866 P50866]
+* '''UniProt:''' [http://www.uniprot.org/uniprot/P39754 P39754]
-* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28220]
+* '''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===
+:* 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=
-* '''Operon:'''
+* '''Operon:''' ''[[ybbP]]-[[ybbR]]-[[glmM]]-[[glmS]]''
+* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=glmS_200277_202079_1 glmS] {{PubMed|22383849}}
-* '''[[Sigma factor]]:'''
+* '''Sigma factor:''' [[SigA]] {{PubMed|22211522}}
 * '''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]
+** 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 =
-* '''Mutant:''' ''clpX::kan'', ''clpX::spec'' and ''clpX::cat'' available from the [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab
+* '''Mutant:'''
 * '''Expression vector:'''
@@ Line 111: / Line 146: @@
 * '''lacZ fusion:'''
-* '''GFP fusion:''' C-terminal GFP fusions (both single copy and 2th copy in ''amyE'' locus, also as CFP and YFP variants) available from the [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab
+* '''GFP fusion:'''
 * '''two-hybrid system:'''
@@ Line 118: / Line 153: @@
 =Labs working on this gene/protein=
-[[Leendert Hamoen]], Newcastle University, UK [http://www.ncl.ac.uk/camb/staff/profile/l.hamoen homepage]
+[[Wade Winkler]], University of Texas, USA, [http://www.utsouthwestern.edu/findfac/professional/0,,68018,00.html Homepage]
 =Your additional remarks=
 =References=
+==Reviews==
+<pubmed> 18279655 </pubmed>
-<pubmed> 19136590 , 9643546, 18786145 </pubmed>
+==The ''glmS'' Ribozyme==
+<pubmed>18079181 ,16484375, 16784238 ,15096624 , 16990543 ,17114942 ,16484375 , 15029187, 17283212 , 16298301, 19228039 21317896 21395279 </pubmed>
-# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+==Other Original Publications==
+'''Additional publications:''' {{PubMed|22211522}}
+<pubmed> 14343123 17981983 ,11160890, 18295797 20525796  </pubmed>
+[[Category:Protein-coding genes]]

Difference between revisions of "Sandbox"

Latest revision as of 13:22, 29 July 2014

Contents

Categories containing this gene/protein

This gene is a member of the following regulons

The gene

Basic information

Phenotypes of a mutant

Database entries

Additional information

The protein

Basic information/ Evolution

Extended information on the protein

Database entries

Additional information

Expression and regulation

Biological materials

Labs working on this gene/protein

Your additional remarks

References

Reviews

The glmS Ribozyme

Other Original Publications

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