Refined structures at 2 and 2.2 Å resolution of two forms of the H-protein, a lipoamide-containing protein of the glycine decarboxylase complex

H-protein, a 14 kDa lipoic acid-containing protein is a component of the glycine decarboxylase complex. This complex which consists of four protein components (P-, H-, T- and L-protein) catalyzes the oxidative decarboxylation of glycine. The mechanistic heart of the complex is provided by the lipoic acid attached to a lysine residue of the H-protein. It undergoes a cycle of transformations, i.e. reductive methylamination, methylamine transfer, and electron transfer. We present details of the crystal structures of the H-protein, in its two forms, H-Pro_Ox with oxidized lipoamide and H-Pro_Met with methylamine-loaded lipoamide. X-ray diffraction data were collected from crystals of H-Pro_Ox to 2 and H-Pro_Met to 2.2 Å resolution. The final R-factor value for the H-Pro_Ox is 18.5% for data with F > 2σ. in the range of 8.0–2.0 Å resolution. The refinement confirmed our previous model, refined to 2.6 Å, of a β-fold sandwich structure with two β-sheets. The lipoamide arm attached to Lys63, located in the loop of a hairpin conformation, is clearly visible at the surface of the protein. The H-Pro_Met has been crystallized in orthorhombic and monoclinic forms and the structures were solved by molecular replacement, starting from the H-Pro_Ox model. The orthorhombic structure has been refined with a final R-factor value of 18.5% for data with F > 2σ in the range of 8.0–2.2 Å resolution. The structure of the monoclinic form has been refined with a final R-factor value of 17.5% for data with F > 2σ in the range of 15.0–3.0 Å. In these two structures which have similar packing, the protein conformation is identical to the conformation found in the H-Pro_Ox. The main change lies in the position of the lipoamide group which has moved significantly when loaded with methylamine. In this case the methylamine-lipoamide group is tucked into a cleft at the surface of the protein where it is stabilized by hydrogen bonds and hydrophobic contacts. Thus, it is totally protected and not free to move in aqueous solvent. In addition, the H-protein presents some sequence and structural analogies with other lipoate- and biotin-containing proteins and also with proteins of the phosphoenolpyruvate:sugar phosphotransferase system.