title: Structural similarity of YbeD protein from Escherichia coli to allosteric regulatory domains.
abstract: 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.
authors.affiliation: Department of Biochemistry, McGill University, Montreal, Quebec, Canada H3G 1Y6.
authors.forename: Guennadi
authors.initials: G
authors.lastname: Kozlov
authors.forename: Demetra
authors.initials: D
authors.lastname: Elias
authors.forename: Anthony
authors.initials: A
authors.lastname: Semesi
authors.forename: Adelinda
authors.initials: A
authors.lastname: Yee
authors.forename: Miroslaw
authors.initials: M
authors.lastname: Cygler
authors.forename: Kalle
authors.initials: K
authors.lastname: Gehring
mesh_terms: 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*
chemical_list: D029968:Escherichia coli Proteins; D008063:Thioctic Acid; D046929:Serine-Type D-Ala-D-Ala Carboxypeptidase