Difference between revisions of "DefB"

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* '''Description:''' major formylmethionine deformylase <br/><br/>
+
* '''Description:''' N-formylcysteine deformylase, required for the conversion of S-methyl-cysteine to cysteine<br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || formylmethionine deformylase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || N-formylcysteine deformylase
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[translation]]
+
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of S-methyl-cysteine
 
|-
 
|-
 
|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=BSU14560 ykrB]
 
|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=BSU14560 ykrB]
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= [[Categories]] containing this gene/protein =
 
= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[translation]]}},
+
{{SubtiWiki category|[[sulfur metabolism]]}}
{{SubtiWiki category|[[protein modification]]}}
 
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
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===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
* no growth with S-methyl cysteine {{PubMed|23944997}}
  
 
=== Database entries ===
 
=== Database entries ===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
* '''Catalyzed reaction/ biological activity:''' Formyl-L-methionyl peptide + H<sub>2</sub>O = formate + methionyl peptide (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:''' N-acetylcystein --> cysteine + acetate {{PubMed|23944997}}
  
 
* '''Protein family:''' polypeptide deformylase family (according to Swiss-Prot)
 
* '''Protein family:''' polypeptide deformylase family (according to Swiss-Prot)
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* '''Operon:'''  
 
* '''Operon:'''  
  
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=defB_1526195_1526749_-1 ykrB] {{PubMed|22383849}}
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=defB_1526195_1526749_-1 defB] {{PubMed|22383849}}
  
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
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=References=
 
=References=
  
<pubmed>11429456,, </pubmed>
+
<pubmed>11429456,23944997, </pubmed>
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 10:47, 18 August 2013

  • Description: N-formylcysteine deformylase, required for the conversion of S-methyl-cysteine to cysteine

Gene name ykrB
Synonyms defB
Essential no
Product N-formylcysteine deformylase
Function utilization of S-methyl-cysteine
Gene expression levels in SubtiExpress: ykrB
MW, pI 20 kDa, 5.456
Gene length, protein length 552 bp, 184 aa
Immediate neighbours ykrA, ykzV
Sequences Protein DNA DNA_with_flanks
Genetic context
YkrB context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
YkrB expression.png















Categories containing this gene/protein

sulfur metabolism

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag: BSU14560

Phenotypes of a mutant

  • no growth with S-methyl cysteine PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: N-acetylcystein --> cysteine + acetate PubMed
  • Protein family: polypeptide deformylase 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: 1LQY (complex with antibiotic actinonin, Geobacillus stearothermophilus)
  • KEGG entry: [2]

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

Che-Man Chan, Antoine Danchin, Philippe Marlière, Agnieszka Sekowska
Paralogous metabolism: S-alkyl-cysteine degradation in Bacillus subtilis.
Environ Microbiol: 2014, 16(1);101-17
[PubMed:23944997] [WorldCat.org] [DOI] (I p)

Michael Haas, Dieter Beyer, Reinhold Gahlmann, Christoph Freiberg
YkrB is the main peptide deformylase in Bacillus subtilis, a eubacterium containing two functional peptide deformylases.
Microbiology (Reading): 2001, 147(Pt 7);1783-1791
[PubMed:11429456] [WorldCat.org] [DOI] (P p)