Difference between revisions of "Sandbox"

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* '''Description:''' IMP dehydrogenase <br/><br/>
+
* '''Description:''' [[penicillin-binding protein]] 5*, D-alanyl-D-alanine carboxypeptidase <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'''
−
|''guaB''
+
|''dacA''
−
|-
 
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''guaA ''
 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || IMP dehydrogenase
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of GMP
+
|style="background:#ABCDEF;" align="center"| '''Product''' || [[penicillin-binding protein]] 5*, <br/>D-alanyl-D-alanine carboxypeptidase
 
|-
 
|-
−
|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=BSU00090 GuaB]
+
|style="background:#ABCDEF;" align="center"|'''Function''' || carboxypeptidase
 
|-
 
|-
−
|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/purine_biosynthesis.html Purine synthesis], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)]'''
+
|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=BSU00100 dacA]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 6.168  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 5.668  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1464 bp, 488 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1329 bp, 443 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaC]]'', ''[[dacA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[guaB]]'', ''[[pdxS]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00090 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00090 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00090 DNA_with_flanks]
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00100 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00100 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00100 DNA_with_flanks]
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:guaB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:dacA_context.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=guaB_15915_17381_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:guaB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00090]]
+
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dacA_17534_18865_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:dacA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00100]]
 
|-
 
|-
 
|}
 
|}
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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/>
  
 
= [[Categories]] containing this gene/protein =
 
= [[Categories]] containing this gene/protein =
−
{{SubtiWiki category|[[biosynthesis/ acquisition of nucleotides]]}},
+
{{SubtiWiki category|[[cell wall synthesis]]}},
−
{{SubtiWiki category|[[essential genes]]}},
+
{{SubtiWiki category|[[membrane proteins]]}}
−
{{SubtiWiki category|[[phosphoproteins]]}}
 
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
−
{{SubtiWiki regulon|[[CodY regulon]]}}
+
 
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00090
+
* '''Locus tag:''' BSU00100
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/guaB.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10073]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10074]
  
 
=== Additional information===
 
=== Additional information===
 +
 +
  
  
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Inosine 5'-phosphate + NAD<sup>+</sup> + H<sub>2</sub>O = xanthosine 5'-phosphate + NADH (according to Swiss-Prot)  
+
* '''Catalyzed reaction/ biological activity:''' Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala (according to Swiss-Prot)  
  
−
* '''Protein family:''' IMPDH/GMPR family (according to Swiss-Prot)
+
* '''Protein family:''' peptidase S11 family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''  
+
* '''Modification:'''
−
** phosphorylated (STY) [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
 
−
** Cys308 is S-cysteinylated after diamide stress [http://www.ncbi.nlm.nih.gov/pubmed/17611193 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
 
−
** Cys308 is S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species [http://www.ncbi.nlm.nih.gov/pubmed/22938038 PubMed]
 
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
−
** inhibition of enzymatic activity by (p)ppGpp during the ´stringent response´{{PubMed|22981860,6111556}}
 
  
 
* '''[[SubtInteract|Interactions]]:'''
 
* '''[[SubtInteract|Interactions]]:'''
  
−
* '''[[Localization]]:'''
+
* '''[[Localization]]:'''  
 +
** secreted (according to Swiss-Prot),  membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1VRD 1VRD] (from ''Thermotoga maritima msb8'', 60% identity, 80% similarity)
+
* '''Structure:'''
  
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/P21879 P21879]
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P08750 P08750]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00090]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00100]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.205 1.1.1.205]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''guaB'' {{PubMed|22383849}}
+
* '''Operon:'''  
  
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=guaB_15915_17381_1 guaB] {{PubMed|22383849}}
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dacA_17534_18865_1 dacA] {{PubMed|22383849}}
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
−
** activated during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
 
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
−
** [[CodY]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
 
  
−
* '''Additional information:'''
+
* '''Additional information:'''
−
** the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
 
−
** inhibition of enzymatic activity by (p)ppGpp during the ´stringent response´{{PubMed|6111556}}
 
  
 
=Biological materials =
 
=Biological materials =
  
 
* '''Mutant:'''
 
* '''Mutant:'''
 +
** 1A742 ( ''dacA''::''cat''), {{PubMed|3087956}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A742&Search=1A742 BGSC]
 +
** 1A743 ( ''dacA''::''cat''), {{PubMed|3087956}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A743&Search=1A743 BGSC]
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
−
** purification from ''B. subtilis'' with an N-terminal Strep-tag, for [[SPINE]], (in [[pGP380]]): pGP901, available in [[Stülke]] lab
 
 
          
 
          
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
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=References=
 
=References=
  
−
<pubmed>22938038,17611193,12884008,1722815, 22981860,12618455,17726680 17726680 6111556 </pubmed>
+
<pubmed>,9864321,18763711, 23531131 </pubmed>
−
 
 
−
[http://www.ncbi.nlm.nih.gov/pubmed/PMID PubMed]
 
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 14:54, 11 November 2013

Gene name dacA
Synonyms
Essential no
Product penicillin-binding protein 5*,
D-alanyl-D-alanine carboxypeptidase
Function carboxypeptidase
Gene expression levels in SubtiExpress: dacA
MW, pI 48 kDa, 5.668
Gene length, protein length 1329 bp, 443 aa
Immediate neighbours guaB, pdxS
Sequences Protein DNA DNA_with_flanks
Genetic context
DacA context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
DacA expression.png















Categories containing this gene/protein

cell wall synthesis, membrane proteins

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag: BSU00100

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala (according to Swiss-Prot)
  • Protein family: peptidase S11 family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Your additional remarks

References

Elitza I Tocheva, Javier López-Garrido, H Velocity Hughes, Jennifer Fredlund, Erkin Kuru, Michael S Vannieuwenhze, Yves V Brun, Kit Pogliano, Grant J Jensen
Peptidoglycan transformations during Bacillus subtilis sporulation.
Mol Microbiol: 2013, 88(4);673-86
[PubMed:23531131] [WorldCat.org] [DOI] (I p)

Hannes Hahne, Susanne Wolff, Michael Hecker, Dörte Becher
From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches.
Proteomics: 2008, 8(19);4123-36
[PubMed:18763711] [WorldCat.org] [DOI] (I p)

D L Popham, M E Gilmore, P Setlow
Roles of low-molecular-weight penicillin-binding proteins in Bacillus subtilis spore peptidoglycan synthesis and spore properties.
J Bacteriol: 1999, 181(1);126-32
[PubMed:9864321] [WorldCat.org] [DOI] (P p)

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