Difference between revisions of "Sandbox"
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− | * '''Description:''' glutamine-fructose-6-phosphate transaminase | + | * '''Description:''' glutamine-fructose-6-phosphate transaminase <br/><br/> |
− | {| align="right" border="1" cellpadding="2" |- |style="background:#ABCDEF;" align="center"|'''Gene name''' |''glmS'' |- |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"| '''Product''' || glutamine-fructose-6-phosphate transaminase |- |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]]: | + | {| align="right" border="1" cellpadding="2" |
− | [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]''' |- |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 65 kDa, 4.796 |- |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1800 bp, 600 aa |- |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+ | + | |- |
− | (Barbe ''et al.'', 2009)''' |- |colspan="2" | '''Genetic context''' | + | |style="background:#ABCDEF;" align="center"|'''Gene name''' |
− | [[Image:glmS_context.gif]] | + | |''glmS'' |
− | This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList] | + | |- |
− | |- |colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=glmS_200277_202079_1 Expression at a glance]''' | + | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''gcaA, ybxD '' |
− | [[Image:glmS_expression.png|500px]] |- |} | + | |- |
+ | |style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed] | ||
+ | |- | ||
+ | |style="background:#ABCDEF;" align="center"| '''Product''' || glutamine-fructose-6-phosphate transaminase | ||
+ | |- | ||
+ | |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/murein/index.html Murein recycling]''' | ||
+ | |- | ||
+ | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 65 kDa, 4.796 | ||
+ | |- | ||
+ | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1800 bp, 600 aa | ||
+ | |- | ||
+ | |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+[EMBLCDS:CAB11954]+-newId sequences] <br/> (Barbe ''et al.'', 2009)''' | ||
+ | |- | ||
+ | |colspan="2" | '''Genetic context''' <br/> [[Image:glmS_context.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]'''   {{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= | ||
+ | === Basic information === | ||
+ | * '''Locus tag:''' BSU01780 | ||
+ | ===Phenotypes of a mutant === | ||
+ | essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed] | ||
+ | === Database entries === | ||
+ | * '''DBTBS entry:''' no entry | ||
+ | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10948] | ||
+ | === 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:''' | |
− | [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/P39754 P39754] * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01780] * '''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:''' ''[[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:''' [[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:''' ''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}} =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, [http://www.utsouthwestern.edu/findfac/professional/0,,68018,00.html Homepage] =Your additional remarks= =References= ==Reviews== 18279655 ==The ''glmS'' Ribozyme== 18079181 ,16484375, 16784238 ,15096624 , 16990543 ,17114942 ,16484375 , 15029187, 17283212 , 16298301, 19228039 21317896 21395279 ==Other Original Publications== '''Additional publications:''' {{PubMed|22211522}} 14343123 17981983 ,11160890, 18295797 20525796 [[Category:Protein-coding genes]] | + | |
+ | * '''Domains:''' | ||
+ | |||
+ | * '''Modification:''' | ||
+ | |||
+ | * '''Cofactor(s):''' | ||
+ | |||
+ | * '''Effectors of protein activity:''' | ||
+ | |||
+ | * '''[[SubtInteract|Interactions]]:''' | ||
+ | |||
+ | * '''[[Localization]]:''' | ||
+ | ** cytoplasm (according to Swiss-Prot) | ||
+ | |||
+ | === Database entries === | ||
+ | |||
+ | * '''Structure:'''[http://www.pdb.org/pdb/explore/explore.do?structureId=HIV HIV] (from ''Bacillus subtilis'', 100% identity) {{PubMed|13454352}}</br> [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/P39754 P39754] | ||
+ | |||
+ | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01780] | ||
+ | |||
+ | * '''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:''' ''[[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:''' [[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:''' ''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}} | ||
+ | |||
+ | =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, [http://www.utsouthwestern.edu/findfac/professional/0,,68018,00.html Homepage] | ||
+ | |||
+ | =Your additional remarks= | ||
+ | |||
+ | =References= | ||
+ | ==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]] |
Revision as of 13:56, 25 November 2013
- Description: glutamine-fructose-6-phosphate transaminase
Gene name | 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: Murein recycling | |
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 This image was kindly provided by SubtiList
| |
Expression at a glance PubMed |
Contents
Categories containing this gene/protein
cell wall synthesis, biosynthesis of cell wall components, essential genes
This gene is a member of the following regulons
The gene
Basic information
- Locus tag: BSU01780
Phenotypes of a mutant
essential PubMed
Database entries
- 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:
- Localization:
- cytoplasm (according to Swiss-Prot)
Database entries
- Structure:HIV (from Bacillus subtilis, 100% identity) PubMed</br> 2VF4 (GlmS from E. coli, 39% identity, 58% similarity) PubMed
- 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
- Regulation:
- 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:
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
Other Original Publications
Additional publications: PubMed