2C31

CRYSTAL STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH THE COFACTOR DERIVATIVE THIAMIN-2-THIAZOLONE DIPHOSPHATE AND ADENOSINE DIPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for Activation of the Thiamin Diphosphate-Dependent Enzyme Oxalyl-Coa Decarboxylase by Adenosine Diphosphate.

Berthold, C.L.Moussatche, P.Richards, N.G.J.Lindqvist, Y.

(2005) J.Biol.Chem. 280: 41645

  • DOI: 10.1074/jbc.M509921200

  • PubMed Abstract: 
  • Oxalyl-coenzyme A decarboxylase is a thiamin diphosphate-dependent enzyme that plays an important role in the catabolism of the highly toxic compound oxalate. We have determined the crystal structure of the enzyme from Oxalobacter formigenes from a h ...

    Oxalyl-coenzyme A decarboxylase is a thiamin diphosphate-dependent enzyme that plays an important role in the catabolism of the highly toxic compound oxalate. We have determined the crystal structure of the enzyme from Oxalobacter formigenes from a hemihedrally twinned crystal to 1.73 A resolution and characterized the steady-state kinetic behavior of the decarboxylase. The monomer of the tetrameric enzyme consists of three alpha/beta-type domains, commonly seen in this class of enzymes, and the thiamin diphosphate-binding site is located at the expected subunit-subunit interface between two of the domains with the cofactor bound in the conserved V-conformation. Although oxalyl-CoA decarboxylase is structurally homologous to acetohydroxyacid synthase, a molecule of ADP is bound in a region that is cognate to the FAD-binding site observed in acetohydroxyacid synthase and presumably fulfils a similar role in stabilizing the protein structure. This difference between the two enzymes may have physiological importance since oxalyl-CoA decarboxylation is an essential step in ATP generation in O. formigenes, and the decarboxylase activity is stimulated by exogenous ADP. Despite the significant degree of structural conservation between the two homologous enzymes and the similarity in catalytic mechanism to other thiamin diphosphate-dependent enzymes, the active site residues of oxalyl-CoA decarboxylase are unique. A suggestion for the reaction mechanism of the enzyme is presented.


    Related Citations: 
    • Detection and Characterization of Merohedral Twinning in Crystals of Oxalyl-Coenzyme a Decarboxylase from Oxalobacter Formigenes.
      Berthold, C.L.,Sidhu, H.,Ricagno, S.,Richards, N.G.J.,Lindqvist, Y.
      (2006) Biochim.Biophys.Acta 1764: 122


    Organizational Affiliation

    Molecular Structural Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OXALYL-COA DECARBOXYLASE
A, B
568Oxalobacter formigenesMutation(s): 0 
Gene Names: oxc
EC: 4.1.1.8
Find proteins for P40149 (Oxalobacter formigenes)
Go to UniProtKB:  P40149
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TZD
Query on TZD

Download SDF File 
Download CCD File 
A, B
2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE
THIAMIN THIAZOLONE DIPHOSPHATE
C12 H18 N4 O8 P2 S
ZGJUYGIRPQSCFA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.150 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 124.300α = 90.00
b = 124.300β = 90.00
c = 151.700γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
CNSrefinement
MOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-07
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance