1DXM

Reduced form of the H protein from glycine decarboxylase complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Interaction between the Lipoamide-Containing H-Protein and the Lipoamide Dehydrogenase (L-Protein) of the Glycine Decarboxylase Multienzyme System. 2. Crystal Structure of H- and L-Proteins

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

(2000) Eur.J.Biochem. 267: 2890

  • Primary Citation of Related Structures:  1DXL

  • PubMed 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) int ...

    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. (2000) Eur. J. Biochem. 267, 2882-2889] and by small angle X-ray scattering experiments reported herein.


    Related Citations: 
    • 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
      Pares, S.,Cohen-Addad, C.,Sieker, L.,Neuburger, M.,Douce, R.
      (1995) Acta Crystallogr.,Sect.D D51: 1041
    • The Lipoamide Arm in the Glycine Decarboxylase is not Freely Swinging
      Cohen-Addad, C.,Pares, S.,Sieker, L.,Neuburger, M.,Douce, R.
      (1995) Nat.Struct.Mol.Biol. 2: 63
    • Structural Studies of the Glycine Decarboxylase Complex from Pea Leaf Mitochondria
      Cohen-Addad, C.,Faure, M.,Neuburger, M.,Ober, R.,Sieker, L.,Bourguignon, J.,Macherel, D.,Douce, R.
      (1997) Biochimie 79: 637


    Organizational Affiliation

    Institut de Biologie Structurale Jean-Pierre Ebel, CEA/CNRS/Université Joseph Fourier, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H PROTEIN
A, B
131Pisum sativumGene Names: GDCSH (GCDH)
Find proteins for P16048 (Pisum sativum)
Go to UniProtKB:  P16048
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RED
Query on RED

Download SDF File 
Download CCD File 
A, B
DIHYDROLIPOIC ACID
C8 H16 O2 S2
IZFHEQBZOYJLPK-SSDOTTSWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.204 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 56.410α = 90.00
b = 56.410β = 90.00
c = 135.170γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-07-04
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance