Dihydrolipoamide dehydrogenase of glycine decarboxylase from Pisum Sativum

Experimental Data Snapshot

  • Resolution: 3.15 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

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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

  • DOI: https://doi.org/10.1046/j.1432-1033.2000.01330.x
  • Primary Citation of Related Structures:  
    1DXL, 1DXM

  • 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) 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
470Pisum sativumMutation(s): 0 
Find proteins for P31023 (Pisum sativum)
Explore P31023 
Go to UniProtKB:  P31023
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31023
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.15 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.56α = 90
b = 108.33β = 90
c = 202.19γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-07-20
    Type: Initial release
  • Version 1.1: 2014-02-19
    Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Version format compliance
  • Version 1.2: 2023-12-06
    Changes: Data collection, Database references, Derived calculations, Refinement description