Difference between revisions of "DapI"

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* '''Description:''' write here <br/><br/>
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* '''Description:''' N-acetyl-diaminopimelate deacetylase<br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
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|''ykuR''
 
|''ykuR''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' dapL''
 
|-
 
|-
 
|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]  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' ||  
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|style="background:#ABCDEF;" align="center"| '''Product''' || N-acetyl-diaminopimelate deacetylase
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
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|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of lysine and peptidoglycan
 +
|-
 +
|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=BSU14190 dapI]
 +
|-
 +
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=DapI DapI]
 +
|-
 +
|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=DapI DapI]'''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.102   
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.102   
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuQ]]'', ''[[ykuS]]''
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuQ]]'', ''[[ykuS]]''
 
|-
 
|-
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ykuR_nucleotide.txt    Gene sequence     (+200bp)  ]'''
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|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU14190 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU14190 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU14190 DNA_with_flanks]
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ykuR_protein.txt Protein sequence]'''
 
 
|-
 
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ykuR_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ykuR_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=dapL_1489753_1490877_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ykuR_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14190]]
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
 +
<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|[[biosynthesis/ acquisition of amino acids]]}},
 +
{{SubtiWiki category|[[essential genes]]}}
 +
 +
= This gene is a member of the following [[regulons]] =
  
−
<br/><br/>
 
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Locus tag:''' BSU14190
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
+
* essential {{PubMed|24261876,12682299}}
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
* depletion of DapI results in swelling and rounding up of cells prior to lysis {{PubMed|24261876}}
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ykuR.html]
+
* '''DBTBS entry:''' no entry
  
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13302]
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13302]
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' N-acetyl-LL-2,6-diaminopimelate + H<sub>2</sub>O --> acetate + LL-2,6-diaminopimelate {{PubMed|24261876}}
  
−
* '''Protein family:'''
+
* '''Protein family:''' peptidase M20A family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):'''
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* '''Paralogous protein(s):''' [[SndA]], [[SndB]], [[SndC]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:'''  
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* '''[[Domains]]:'''  
  
 
* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):'''
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* '''[[Cofactors]]:'''
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
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* '''Interactions:'''
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* '''[[SubtInteract|Interactions]]:'''
 +
** forms dimers {{PubMed|24261876}}
 +
** [[DapI]]-[[MreB]] {{PubMed|24261876}}
  
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* '''Localization:'''
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* '''[[Localization]]:'''
 +
** forms uniformly distributed foci in the cytoplasm {{PubMed|24261876}}
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
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* '''Swiss prot entry:'''
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* '''UniProt:''' [http://www.uniprot.org/uniprot/O34916 O34916]
  
−
* '''KEGG entry:'''
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* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14190]
  
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* '''E.C. number:'''
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* '''E.C. number:''' [http://www.expasy.org/enzyme/3.5.1.47 3.5.1.47]
  
 
=== Additional information===
 
=== Additional information===
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* '''Operon:'''  
 
* '''Operon:'''  
  
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* '''Sigma factor:'''  
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* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dapL_1489753_1490877_1 dapI] {{PubMed|22383849}}
 +
 
 +
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
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* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
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* '''Additional information:'''  
+
* '''Additional information:'''
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium): 274 {{PubMed|24696501}}
 +
** number of protein molecules per cell (complex medium with amino acids, without glucose): 637 {{PubMed|24696501}}
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
−
 
+
<pubmed>24261876 </pubmed>
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
[[Category:Protein-coding genes]]

Latest revision as of 11:25, 17 April 2014

  • Description: N-acetyl-diaminopimelate deacetylase

Gene name ykuR
Synonyms dapL
Essential yes PubMed
Product N-acetyl-diaminopimelate deacetylase
Function biosynthesis of lysine and peptidoglycan
Gene expression levels in SubtiExpress: dapI
Interactions involving this protein in SubtInteract: DapI
Metabolic function and regulation of this protein in SubtiPathways:
DapI
MW, pI 41 kDa, 5.102
Gene length, protein length 1122 bp, 374 aa
Immediate neighbours ykuQ, ykuS
Sequences Protein DNA DNA_with_flanks
Genetic context
YkuR context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
YkuR expression.png















Categories containing this gene/protein

cell wall synthesis, biosynthesis of cell wall components, biosynthesis/ acquisition of amino acids, essential genes

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag: BSU14190

Phenotypes of a mutant

  • essential PubMed
  • depletion of DapI results in swelling and rounding up of cells prior to lysis PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: N-acetyl-LL-2,6-diaminopimelate + H2O --> acetate + LL-2,6-diaminopimelate PubMed
  • Protein family: peptidase M20A family (according to Swiss-Prot)

Extended information on the protein

  • Kinetic information:
  • Modification:
  • Effectors of protein activity:

Database entries

  • Structure:
  • KEGG entry: [2]

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:
    • number of protein molecules per cell (minimal medium with glucose and ammonium): 274 PubMed
    • number of protein molecules per cell (complex medium with amino acids, without glucose): 637 PubMed

Biological materials

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

Labs working on this gene/protein

Your additional remarks

References

Anne-Stéphanie Rueff, Arnaud Chastanet, Julia Domínguez-Escobar, Zhizhong Yao, James Yates, Maria-Victoria Prejean, Olivier Delumeau, Philippe Noirot, Roland Wedlich-Söldner, Sergio R Filipe, Rut Carballido-López
An early cytoplasmic step of peptidoglycan synthesis is associated to MreB in Bacillus subtilis.
Mol Microbiol: 2014, 91(2);348-62
[PubMed:24261876] [WorldCat.org] [DOI] (I p)

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