Prediction of the three-dimensional structures of the biotinylated domain from yeast pyruvate carboxylase and of the lipoylated H-protein from the pea leaf glycine cleavage system: a new automated method for the prediction of protein tertiary structure

Protein Sci. 1993 Apr;2(4):626-39. doi: 10.1002/pro.5560020413.


A new, automated, knowledge-based method for the construction of three-dimensional models of proteins is described. Geometric restraints on target structures are calculated from a consideration of homologous template structures and the wider knowledge base of unrelated protein structures. Three-dimensional structures are calculated from initial partly folded states by high-temperature molecular dynamics simulations followed slow cooling of the system (simulated annealing) using nonphysical potentials. Three-dimensional models for the biotinylated domain from the pyruvate carboxylase of yeast and the lipoylated H-protein from the glycine cleavage system of pea leaf were constructed, based on the known structures of two lipoylated domains of 2-oxo acid dehydrogenase multienzyme complexes. Despite their weak sequence similarity, the three proteins are predicted to have similar three-dimensional structures, representative of a new protein module. Implications for the mechanisms of posttranslational modification of these proteins and their catalytic function are discussed.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Oxidoreductases*
  • Amino Acid Sequence
  • Carrier Proteins / chemistry*
  • Fabaceae / chemistry
  • Glycine Decarboxylase Complex H-Protein
  • Glycine Dehydrogenase (Decarboxylating)
  • Hydrogen Bonding
  • Models, Molecular
  • Molecular Sequence Data
  • Plants, Medicinal
  • Protein Structure, Tertiary
  • Pyruvate Carboxylase / chemistry*
  • Saccharomyces cerevisiae / enzymology
  • Saccharomyces cerevisiae Proteins
  • Sequence Alignment


  • Carrier Proteins
  • Glycine Decarboxylase Complex H-Protein
  • Saccharomyces cerevisiae Proteins
  • Amino Acid Oxidoreductases
  • GCV2 protein, S cerevisiae
  • Glycine Dehydrogenase (Decarboxylating)
  • Pyruvate Carboxylase