Structural similarity of YbeD protein from Escherichia coli to allosteric regulatory domains

J Bacteriol. 2004 Dec;186(23):8083-8. doi: 10.1128/JB.186.23.8083-8088.2004.


Lipoic acid is an essential prosthetic group in several metabolic pathways. The biosynthetic pathway of protein lipoylation in Escherichia coli involves gene products of the lip operon. YbeD is a conserved bacterial protein located in the dacA-lipB intergenic region. Here, we report the nuclear magnetic resonance structure of YbeD from E. coli. The structure includes a beta alpha beta beta alpha beta fold with two alpha-helices on one side of a four-strand antiparallel beta-sheet. The beta 2-beta 3 loop shows the highest sequence conservation and is likely functionally important. The beta-sheet surface contains a patch of conserved hydrophobic residues, suggesting a role in protein-protein interactions. YbeD shows striking structural homology to the regulatory domain from d-3-phosphoglycerate dehydrogenase, hinting at a role in the allosteric regulation of lipoic acid biosynthesis or the glycine cleavage system.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Allosteric Regulation
  • Amino Acid Sequence
  • Escherichia coli Proteins / chemistry*
  • Molecular Sequence Data
  • Nuclear Magnetic Resonance, Biomolecular
  • Protein Structure, Secondary
  • Serine-Type D-Ala-D-Ala Carboxypeptidase / chemistry*
  • Thioctic Acid / biosynthesis*


  • Escherichia coli Proteins
  • Thioctic Acid
  • Serine-Type D-Ala-D-Ala Carboxypeptidase

Associated data

  • PDB/1RWU