YkfB

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  • Description: L-Ala-D/L-Glu epimerase

Gene name ykfB
Synonyms
Essential no
Product L-Ala-D/L-Glu epimerase
Function cell wall metabolism
Gene expression levels in SubtiExpress: ykfB
MW, pI 39 kDa, 5.905
Gene length, protein length 1098 bp, 366 aa
Immediate neighbours ykfA, ykfC
Sequences Protein DNA Advanced_DNA
Genetic context
YkfB context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
YkfB expression.png















Categories containing this gene/protein

cell wall/ other

This gene is a member of the following regulons

CodY regulon

The gene

Basic information

  • Locus tag: BSU12980

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure: 1TKK (complex with substrate), 1JPM
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulatory mechanism: CodY: transcription repression PubMed
  • 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

Tiit Lukk, Ayano Sakai, Chakrapani Kalyanaraman, Shoshana D Brown, Heidi J Imker, Ling Song, Alexander A Fedorov, Elena V Fedorov, Rafael Toro, Brandan Hillerich, Ronald Seidel, Yury Patskovsky, Matthew W Vetting, Satish K Nair, Patricia C Babbitt, Steven C Almo, John A Gerlt, Matthew P Jacobson
Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.
Proc Natl Acad Sci U S A: 2012, 109(11);4122-7
[PubMed:22392983] [WorldCat.org] [DOI] (I p)

Vadim A Klenchin, Dawn M Schmidt, John A Gerlt, Ivan Rayment
Evolution of enzymatic activities in the enolase superfamily: structure of a substrate-liganded complex of the L-Ala-D/L-Glu epimerase from Bacillus subtilis.
Biochemistry: 2004, 43(32);10370-8
[PubMed:15301535] [WorldCat.org] [DOI] (P p)

Virginie Molle, Yoshiko Nakaura, Robert P Shivers, Hirotake Yamaguchi, Richard Losick, Yasutaro Fujita, Abraham L Sonenshein
Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis.
J Bacteriol: 2003, 185(6);1911-22
[PubMed:12618455] [WorldCat.org] [DOI] (P p)

A M Gulick, D M Schmidt, J A Gerlt, I Rayment
Evolution of enzymatic activities in the enolase superfamily: crystal structures of the L-Ala-D/L-Glu epimerases from Escherichia coli and Bacillus subtilis.
Biochemistry: 2001, 40(51);15716-24
[PubMed:11747448] [WorldCat.org] [DOI] (P p)

D M Schmidt, B K Hubbard, J A Gerlt
Evolution of enzymatic activities in the enolase superfamily: functional assignment of unknown proteins in Bacillus subtilis and Escherichia coli as L-Ala-D/L-Glu epimerases.
Biochemistry: 2001, 40(51);15707-15
[PubMed:11747447] [WorldCat.org] [DOI] (P p)