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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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.C.Neuburger, M.Douce, R.

(1995) Acta Crystallogr.,Sect.D 51: 1041-1051

  • DOI: 10.1107/S0907444995006421
  • Also Cited By: 1DXM

  • 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 mechanis ...

    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.


    Related Citations: 
    • Crystallographic Data for H-Protein from the Glycine Decarboxylase Complex
      Sieker, L.,Cohen-Addad, C.,Neuburger, M.,Douce, R.
      (1991) J.Mol.Biol. 220: 223
    • The Lipoamide Arm in the Glycine Decarboxylase Complex is not Freely Swinging
      Cohen-Addad, C.,Pares, S.,Sieker, L.,Neuburger, M.,Douce, R.
      (1995) Nat.Struct.Mol.Biol. 2: 1
    • X-Ray Structure Determination at 2.6 Angstroms Resolution of a Lipoate-Containing Protein: The H-Protein of the Glycine Decarboxylase Complex from Pea Leaves
      Pares, S.,Cohen-Addad, C.,Sieker, L.,Neuburger, M.,Douce, R.
      (1994) Proc.Natl.Acad.Sci.USA 91: 4850
    • Cdna Cloning, Primary Structure and Gene Expression for H-Protein, a Component of the Glycine-Cleavage System (Glycine Decarboxylase) of Pea (Pisum Sativum) Leaf Mitochondria
      Macherel, D.,Lebrun, M.,Gagnon, J.,Neuburger, M.,Douce, R.
      (1990) Biochem.J. 268: 783


    Organizational Affiliation

    Institut de Biologie Structurale Jean-Pierre Ebel, Centre National de la Recherche Scientifique/Commissariat l'Energie Atomique, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H PROTEIN OF THE GLYCINE CLEAVAGE SYSTEM
A, B
131Pisum sativumMutation(s): 0 
Gene Names: GDCSH (GCDH)
Find proteins for P16048 (Pisum sativum)
Go to UniProtKB:  P16048
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LPB
Query on LPB

Download SDF File 
Download CCD File 
A
5-[(3S)-1,2-dithiolan-3-yl]pentanoic acid
C8 H14 O2 S2
AGBQKNBQESQNJD-ZETCQYMHSA-N
 Ligand Interaction
LPA
Query on LPA

Download SDF File 
Download CCD File 
B
LIPOIC ACID
5-[(3R)-1,2-dithiolan-3-yl]pentanoic acid
C8 H14 O2 S2
AGBQKNBQESQNJD-SSDOTTSWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.185 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 57.300α = 90.00
b = 57.300β = 90.00
c = 136.800γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-05-08
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-10-05
    Type: Non-polymer description
  • Version 1.4: 2014-04-16
    Type: Derived calculations