PDBsum entry 1dxl

Oxidoreductase

PDB id: 1dxl

Contents

Protein chains

467 a.a. *

Ligands

FAD ×4

Waters ×104

* Residue conservation analysis

PDB id:

1dxl

Name:

Oxidoreductase

Title:

Dihydrolipoamide dehydrogenase of glycine decarboxylase from pisum sativum

Structure:

Dihydrolipoamide dehydrogenase. Chain: a, b, c, d. Synonym: lipoamide dehydrogenase, l protein, e3, dldh, glycine cleavage system l protein. Engineered: yes

Source:

Pisum sativum. Pea. Organism_taxid: 3888. Tissue: leaf. Organelle: mitochondria. Cellular_location: mitochondria. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Biol. unit:

Dimer (from PQS)

Resolution:

3.15Å R-factor: 0.226 R-free: 0.323

Authors:

M.Faure,C.Cohen-Addad,J.Bourguignon,D.Macherel,M.Neuburger,R.Douce

Key ref:

M.Faure et al. (2000). Interaction between the lipoamide-containing H-protein and the lipoamide dehydrogenase (L-protein) of the glycine decarboxylase multienzyme system 2. Crystal structures of H- and L-proteins. Eur J Biochem, 267, 2890-2898. PubMed id: 10806386 DOI: 10.1046/j.1432-1033.2000.01330.x

Date:

10-Jan-00 Release date: 20-Jul-00

Protein chains

P31023  (DLDH_PEA) -  Dihydrolipoyl dehydrogenase, mitochondrial from Pisum sativum

Seq: 501 a.a.

Struc: 467 a.a.

Enzyme reactions

• Enzyme class: E.C.1.8.1.4 - dihydrolipoyl dehydrogenase.
• Pathway: Glycine Cleavage System
• Reaction: N₆-[(R)-dihydrolipoyl]-L-lysyl-[protein] + NAD⁺ = N₆-[(R)-lipoyl]- L-lysyl-[protein] + NADH + H⁺
• Cofactor: FAD

FAD (Bound ligand (Het Group name = FAD) corresponds exactly)

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

reference

DOI no: 10.1046/j.1432-1033.2000.01330.x

Eur J Biochem 267:2890-2898 (2000)

PubMed id: 10806386

Interaction between the lipoamide-containing H-protein and the lipoamide dehydrogenase (L-protein) of the glycine decarboxylase multienzyme system 2. Crystal structures of H- and L-proteins.

M.Faure, J.Bourguignon, M.Neuburger, D.MacHerel, L.Sieker, R.Ober, R.Kahn, C.Cohen-Addad, R.Douce.

ABSTRACT

The glycine decarboxylase complex consists of four different component enzymes (P-, H-, T- and L-proteins). The 14-kDa lipoamide-containing H-protein plays a pivotal role in the complete sequence of reactions as its prosthetic group (lipoic acid) interacts successively with the three other components of the complex and undergoes a cycle of reductive methylamination, methylamine transfer and electron transfer. With the aim to understand the interaction between the H-protein and its different partners, we have previously determined the crystal structure of the oxidized and methylaminated forms of the H-protein. In the present study, we have crystallized the H-protein in its reduced state and the L-protein (lipoamide dehydrogenase or dihydrolipoamide dehydrogenase). The L-protein has been overexpressed in Escherichia coli and refolded from inclusion bodies in an active form. Crystals were obtained from the refolded L-protein and the structure has been determined by X-ray crystallography. This first crystal structure of a plant dihydrolipoamide dehydrogenase is similar to other known dihydrolipoamide dehydrogenase structures. The crystal structure of the H-protein in its reduced form has been determined and compared to the structure of the other forms of the protein. It is isomorphous to the structure of the oxidized form. In contrast with methylaminated H-protein where the loaded lipoamide arm was locked into a cavity of the protein, the reduced lipoamide arm appeared freely exposed to the solvent. Such a freedom is required to allow its targeting inside the hollow active site of L-protein. Our results strongly suggest that a direct interaction between the H- and L-proteins is not necessary for the reoxidation of the reduced lipoamide arm bound to the H-protein. This hypothesis is supported by biochemical data [Neuburger, M., Polidori, A.M., Piètre, E., Faure, M., Jourdain, A., Bourguignon, J., Pucci, B. & Douce, R. and by small angle X-ray scattering experiments reported herein.

Selected figure(s)

Figure 1.
Fig. 1. Stereo view of the dihydrolipoyl H protein structure [reduced form (H[red])]. The molecule b of the asymmetric unit (see text) is shown with the two positions of the reduced lipoamide arm, in the molecule a (in red) andin the molecule b (in green). The position of the arm in its methylaminated form is also represented (in blue) [8,9]. The program O [18] was used for this figure and Figs 4 Go-and 6 Go-.

Figure 5.
Fig. 5 Potential surface of the L-protein and the entrance of the dihydrolipoamide binding site. The surface is coloured according to the charges: dark violet corresponds to positively charged surfaces, red to negatively charged surfaces. Yellow to yellow-green corresponds to hydrophobic surfaces. The program GRASP was used for the drawing [35].

The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (2000, 267, 2890-2898) copyright 2000.

Figures were selected by an automated process.