Crystal Structure of Aminomethyltransferase in Complex with Dihydrolipoyl-H-Protein of the Glycine Cleavage System: IMPLICATIONS FOR RECOGNITION OF LIPOYL PROTEIN SUBSTRATE,DISEASE-RELATED MUTATIONS,AND REACTION MECHANISM*

Aminomethyltransferase, a component of the glycine cleavage system termed T-protein, reversibly catalyzes the degradation of the aminomethyl moiety of glycine attached to the lipoate cofactor of H-protein, resulting in the production of ammonia, 5,10-methylenetetrahydrofolate, and dihydrolipoate-bearing H-protein in the presence of tetrahydrofolate. Several mutations in the human T-protein gene are known to cause nonketotic hyperglycinemia. Here, we report the crystal structure of Escherichia coli T-protein in complex with dihydrolipoate-bearing H-protein and 5-methyltetrahydrofolate, a complex mimicking the ternary complex in the reverse reaction. The structure of the complex shows a highly interacting intermolecular interface limited to a small area and the protein-bound dihydrolipoyllysine arm inserted into the active site cavity of the T-protein. Invariant Arg²⁹² of the T-protein is essential for complex assembly. The structure also provides novel insights in understanding the disease-causing mutations, in addition to the disease-related impairment in the cofactor-enzyme interactions reported previously. Furthermore, structural and mutational analyses suggest that the reversible transfer of the methylene group between the lipoate and tetrahydrofolate should proceed through the electron relay-assisted iminium intermediate formation.     

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.

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.     

Molecular phylogeny of Flaveria as deduced from the analysis of nucleotide sequences encoding the H-protein of the glycine cleavage system

Sequence comparisons have shown that nucleotide sequences of the H-protein, a component of the glycine cleavage system, are only moderately conserved and can be used as molecular markers for intrageneric phylogenetic studies. We have analysed the respective cDNA sequences from 12 species of Flaveria, and a more limited set of gdcsH upstream regions. These data are discussed with respect to a phylogenetic reconstruction of Flaveria, a small genus which includes species of different photo-synthetic types, namely C₃, C₃-C₄, C₄-like and C₄. Our analysis essentially supports an earlier hypothesis, based on morphological and eco-geographical data, of the evolution of Flaveria (Powell 1978). This close agreement shows the usefulness of H-protein nucleotide sequences at a low taxonomic level. Our analysis independently confirms that C₄ photosynthesis has evolved two times in different lineages of Flaveria. Most remarkably, the C₄ taxa of Flaveria appear as derived relative to the C₃-C₄ intermediate taxa, i.e. they probably have common direct predecessors. This is the first direct evidence for a phylo-genetically intermediate position of C₃-C₄ intermediate photosynthesis. Our data also confirm the antiquity of C₃ photosynthesis in Flaveria but suggest that the collection of F.pringlei used in our experiments, although clearly of C₃ photosynthetic metabolism, possibly originated from hybridization with a more advanced taxon.