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

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

Other Original Publications

Additional publications: PubMed

Irnov Irnov, Cynthia M Sharma, Jörg Vogel, Wade C Winkler
Identification of regulatory RNAs in Bacillus subtilis.
Nucleic Acids Res: 2010, 38(19);6637-51
[PubMed:20525796] [WorldCat.org] [DOI] (I p)

Stéphane Mouilleron, Marie-Ange Badet-Denisot, Béatrice Golinelli-Pimpaneau
Ordering of C-terminal loop and glutaminase domains of glucosamine-6-phosphate synthase promotes sugar ring opening and formation of the ammonia channel.
J Mol Biol: 2008, 377(4);1174-85
[PubMed:18295797] [WorldCat.org] [DOI] (I p)

Ulf Gerth, Holger Kock, Ilja Kusters, Stephan Michalik, Robert L Switzer, Michael Hecker
Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis.
J Bacteriol: 2008, 190(1);321-31
[PubMed:17981983] [WorldCat.org] [DOI] (I p)

K Yoshida, K Kobayashi, Y Miwa, C M Kang, M Matsunaga, H Yamaguchi, S Tojo, M Yamamoto, R Nishi, N Ogasawara, T Nakayama, Y Fujita
Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis.
Nucleic Acids Res: 2001, 29(3);683-92
[PubMed:11160890] [WorldCat.org] [DOI] (I p)

C J BATES, C A PASTERNAK
FURTHER STUDIES ON THE REGULATION OF AMINO SUGAR METABOLISM IN BACILLUS SUBTILIS.
Biochem J: 1965, 96(1);147-54
[PubMed:14343123] [WorldCat.org] [DOI] (P p)

@@ Line 1: / Line 1: @@
-* '''Description:''' D-alanine transfer from Dcp to undecaprenol-phosphate <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
-|''dltB''
+|''glmS''
 |-
-|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-4r ''
+|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''' || D-alanine transfer from Dcp to undecaprenol-phosphate
+|style="background:#ABCDEF;" align="center"| '''Product''' || glutamine-fructose-6-phosphate transaminase
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of teichoic acid
+|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
-acid (D-alanyl transfer from Dcp to undecaprenol-phosphate)
 |-
-|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 9.944
+|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"| '''Gene length, protein length''' || 1185 bp, 395 aa
+|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 65 kDa, 4.796
 |-
-|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dltA]]'', ''[[dltC]]''
+|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1800 bp, 600 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:CAB15877&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glmM]]'', ''[[ybbU]]''
 |-
-|colspan="2" | '''Genetic context''' <br/> [[Image:dltB_context.gif]]
+|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" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dltB_3953783_3954970_1 Expression at a glance]'''{{PubMed|22383849}}<br/>[[Image:dltB_expression.png|500px]]
+|-
+|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/>
-__TOC__
-<br/><br/>
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[cell wall synthesis]]}},
-{{SubtiWiki category|[[transporters/ other]]}},
 {{SubtiWiki category|[[biosynthesis of cell wall components]]}},
-{{SubtiWiki category|[[cell envelope stress proteins (controlled by SigM, V, W, X, Y)]]}},
+{{SubtiWiki category|[[essential genes]]}}
-{{SubtiWiki category|[[membrane proteins]]}}
 = This gene is a member of the following [[regulons]] =
-{{SubtiWiki regulon|[[SigD regulon]]}},
+{{SubtiWiki regulon|[[glmS ribozyme]]}}
-{{SubtiWiki regulon|[[SigM regulon]]}},
-{{SubtiWiki regulon|[[SigX regulon]]}},
-{{SubtiWiki regulon|[[Spo0A regulon]]}},
-{{SubtiWiki regulon|[[stringent response]]}},
-{{SubtiWiki regulon|[[YvrHb regulon]]}}
 =The gene=
@@ Line 57: / Line 57: @@
 === Basic information ===
-* '''Locus tag:''' BSU38510
+* '''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/dltABCDE.html]
+* '''DBTBS entry:''' no entry
-* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10550]
+* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10948]
 === Additional information===
 =The protein=
@@ Line 76: / Line 77: @@
 === 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:''' membrane-bound acyltransferase family (according to Swiss-Prot)
+* '''Protein family:'''
 * '''Paralogous protein(s):'''
@@ Line 96: / Line 97: @@
 * '''[[SubtInteract|Interactions]]:'''
 * '''[[Localization]]:'''
-** membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+** 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:'''
+**[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/P39580 P39580]
+* '''UniProt:''' [http://www.uniprot.org/uniprot/P39754 P39754]
-* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU38510]
+* '''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:''' ''[[dltA]]-[[dltB]]-[[dltC]]-[[dltD]]-[[dltE]]'' {{PubMed|7797557}}
-* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dltB_3953783_3954970_1 dltB] {{PubMed|22383849}}
+* '''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:''' [[SigD]] {{PubMed|7797557}}, [[SigM]] {{PubMed|18179421}}, [[SigX]] {{PubMed|14762009}}
+* '''Sigma factor:''' [[SigA]] {{PubMed|22211522}}
 * '''Regulation:'''
-** [[RelA]] dependent downregulation (Class I) during stringent response {{PubMed|11948165}}
+** repressed by glucosamine, N-acetylglucosamine, N-propionylglucosamine or N-formylglucosamine {{PubMed|14343123}}
-** repressed under conditions that trigger sporulation ([[Spo0A]]) {{PubMed|7797557}}
+** ''glmS'' is only expressed in the absence of glucosamine 6-phosphate ([[glmS]] [[ribozyme]])
-** expression is reduced in a [[SigV]] mutant {{PubMed|21926231}}
-* '''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
-** activated by [[YvrHb]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
-** [[Spo0A]]: transcription repression {{PubMed|7797557}}
 * '''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 =
@@ Line 144: / Line 153: @@
 =Labs working on this gene/protein=
+[[Wade Winkler]], University of Texas, USA, [http://www.utsouthwestern.edu/findfac/professional/0,,68018,00.html Homepage]
 =Your additional remarks=
 =References=
-'''Additional publications:''' {{PubMed|21856855,21926231}}
+==Reviews==
-<pubmed>14762009,12028417 ,7797557,18763711, </pubmed>
+<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]]

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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