Difference between revisions of "YkfB"

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=== Database entries ===
 
=== Database entries ===

Revision as of 19:31, 25 October 2012

  • 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
Get the DNA and protein sequences
(Barbe et al., 2009)
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)