PDBsum entry 1hpc

Transit peptide

PDB id: 1hpc

Contents

Protein chains

131 a.a. *

Ligands

LPB

LPA

Waters ×206

* Residue conservation analysis

PDB id:

1hpc

Name:

Transit peptide

Title:

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

Structure:

H protein of the glycine cleavage system. Chain: a, b. Engineered: yes

Source:

Pisum sativum. Pea. Organism_taxid: 3888

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.185

Authors:

S.Pares,C.Cohen-Addad,L.Sieker,M.Neuburger,R.Douce

Key ref:

S.Pares et al. (1995). 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 D Biol Crystallogr, 51, 1041-1051. PubMed id: 15299773 DOI: 10.1107/S0907444995006421

Date:

17-Feb-94 Release date: 08-May-95

Protein chains

P16048  (GCSH_PEA) -  Glycine cleavage system H protein, mitochondrial from Pisum sativum

Seq: 165 a.a.

Struc: 131 a.a.

Enzyme reactions

• Enzyme class: E.C.1.4.4.2 - glycine dehydrogenase (aminomethyl-transferring).
• Pathway: Glycine Cleavage System
• Reaction: N₆-[(R)-lipoyl]-L-lysyl-[glycine-cleavage complex H protein] + glycine + H⁺ = N₆-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[glycine- cleavage complex H protein] + CO2
• Cofactor: Pyridoxal 5'-phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1107/S0907444995006421

Acta Crystallogr D Biol Crystallogr 51:1041-1051 (1995)

PubMed id: 15299773

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.

S.Pares, C.Cohen-Addad, L.C.Sieker, M.Neuburger, R.Douce.

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.

Selected figure(s)

Figure 6.
Fig. 6. H-PrOMet orthorhombic crystl form. Plot of the average B-factor values. Same represenaton as in Fig. 3.

Figure 9.
Fig. 9. Stereo viw of the structure of the H-protein an location of the lipoamide arm. (a H-Proox, (b) H-PrOMet.

Figure 11.
Fig. 11. Connolly surface of the cavity containing the lipoamide group. This cavity is essentially identical in H-PrOMet and H-Proox. The figue was generated with the program MS (Connolly, 1983) and TURBO-FRODO (Roussel & Cambiau, 1989).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1995, 51, 1041-1051) copyright 1995.

Figures were selected by an automated process.