Structural similarity of YbeD protein from Escherichia coli to allosteric regulatory domains.
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.
Kozlov
Guennadi
G
Department of Biochemistry, McGill University, Montreal, Quebec, Canada H3G 1Y6.
Elias
Demetra
D
Semesi
Anthony
A
Yee
Adelinda
A
Cygler
Miroslaw
M
Gehring
Kalle
K
D000494:Allosteric Regulation; D000595:Amino Acid Sequence; D029968:Escherichia coli Proteins / Q000737:chemistry*; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D017433:Protein Structure, Secondary; D046929:Serine-Type D-Ala-D-Ala Carboxypeptidase / Q000737:chemistry*; D008063:Thioctic Acid / Q000096:biosynthesis*
D029968:Escherichia coli Proteins; D008063:Thioctic Acid; D046929:Serine-Type D-Ala-D-Ala Carboxypeptidase