1HPC

REFINED STRUCTURES AT 2 ANGSTROMS AND 2.2 ANGSTROMS OF THE TWO FORMS OF THE H-PROTEIN, A LIPOAMIDE-CONTAINING PROTEIN OF THE GLYCINE DECARBOXYLASE

Summary for 1HPC

• Entry DOI: 10.2210/pdb1hpc/pdb
• Descriptor: H PROTEIN OF THE GLYCINE CLEAVAGE SYSTEM, 5-[(3S)-1,2-dithiolan-3-yl]pentanoic acid, LIPOIC ACID, ... (4 entities in total)
• Functional Keywords: transit peptide
• Biological source: Pisum sativum (pea)
• Cellular location: Mitochondrion: P16048
• Total number of polymer chains: 2
• Total formula weight: 28337.58

Authors

Pares, S.,Cohen-Addad, C.,Sieker, L.,Neuburger, M.,Douce, R. (deposition date: 1994-02-17, release date: 1995-05-08, Last modification date: 2024-10-23)

Primary citation

Pares, S.,Cohen-Addad, C.,Sieker, L.C.,Neuburger, M.,Douce, R.
Refined structures at 2 and 2.2 A resolution of two forms of the H-protein, a lipoamide-containing protein of the glycine decarboxylase complex.
Acta Crystallogr.,Sect.D, 51:1041-1051, 1995

PubMed Abstract: 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 A resolution. The final R-factor value for the H-Pro(Ox) is 18.5% for data with F > 2sigma. in the range of 8.0-2.0 A resolution. The refinement confirmed our previous model, refined to 2.6 A, of a beta-fold sandwich structure with two beta-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 > 2sigma in the range of 8.0-2.2 A resolution. The structure of the monoclinic form has been refined with a final R-factor value of 17.5% for data with F > 2sigma in the range of 15.0-3.0 A. 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.

PubMed: 15299773
DOI: 10.1107/S0907444995006421

Experimental method

X-RAY DIFFRACTION (2 Å)