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Overview for MACiE Entry M0231

Version history

General Information

EC Number: 4.1.1.2 (A member of the Lyases, Carbon-carbon lyases, Carboxy-lyases)

Enzyme Name: oxalate decarboxylase

Biological Species: Bacillus subtilis (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

  • O34714 - Oxalate decarboxylase oxdC

Representative PDB Code: 1uw8 - CRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE (Resolution = 2.0 Å).

Catalytic CATH Codes:

"Other" CATH Codes:

Display structure information

Overall Reaction:

Image of Oxalate

Image of Proton

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Image of Formate

Image of Carbon dioxide

Oxalate
C00209
CHEBI:46904
Proton
C00080
CHEBI:24636
Formate
C00058
CHEBI:30751
Carbon dioxide
C00011
CHEBI:16526

This reaction is irreversible.

Overall Comment: Oxalate decarboxylase contains two manganese centres. It is generally thought that site I (Mn1383) is catalytic and that site II (Mn1384) is structural. Further, this enzyme contains an unusual cofactor in the form of molecular oxygen, which is thought to act as an activator to the Mn(II) centre by increasing its redox potential.


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Stepwise Description of the Reaction

Step 1Oxalate coordinates to the Mn(II) centre.
Step 2Dioxygen forms a bond to the Mn(II) centre through coligation.
Step 3Glu162 activates the Mn(III)-bound oxalate through deprotonation. This causes the oxalate bridging oxygen to transfer an electron to the Mn(III) centre.
Step 4The oxalate radical anion decarboxylates.
Step 5The Mn(II) centre transfers an electron to the formyl intermediate carbon. The newly formed carbanion then deprotonates Glu162.
Step 6Oxygen dissociates from the Mn(III) centre, regenerating the Mn(II) centre. Formate also dissociates, the exact order of dissociation is unclear.
Step 7An acid, assumed to be water, protonates formate.

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Catalytic Residues Involved

Type Number Chain Location of Function
Glu 162 A Side Chain
Arg 92 A Side Chain

Organic Cofactors for M0231

Type Identity Chain
Dixoygen O2 0 Overview

Metal Cofactors for M0231

Type Het group Number Chain
manganese MN 1383 A Overview
manganese MN 1384 A Overview

References

  1. V. J. Just et al. (2004), J. Biol. Chem., 279, 19867-19874. A closed conformation of Bacillus subtilis oxalate decarboxylase OxdC provides evidence for the true identity of the active site.
    Medline: 14871895
  2. A. Angerhofer et al. (2007), J. Phys. Chem. B, 111, 5043-5046. Multifrequency EPR studies on the Mn(II) centers of oxalate decarboxylase.
    Medline: 17444678
  3. M. M. Whittaker et al. (2002), J. Biol. Inorg. Chem., 7, 136-145. Characterization of recombinant barley oxalate oxidase expressed by Pichia pastoris.
    Medline: 11862550
  4. D. Svedruzic et al. (2007), Arch. Biochem. Biophys., 464, 36-47. Investigating the roles of putative active site residues in the oxalate decarboxylase from Bacillus subtilis.
    Medline: 17459326
  5. M. Muthusamy et al. (2006), Biochemistry, 45, 10667-10673. Real-time monitoring of the oxalate decarboxylase reaction and probing hydron exchange in the product, formate, using fourier transform infrared spectroscopy.
    Medline: 16939218
  6. V. J. Just et al. (2007), Biochem. J., 407, 397-406. The identity of the active site of oxalate decarboxylase and the importance of the stability of active-site lid conformations.
    Medline: 17680775

Homologue information for M0231 (1uw8)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
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GOA logo
cytoplasm (cellular component)
lyase activity (molecular function)
carboxy-lyase activity (molecular function)
nutrient reservoir activity (molecular function)
oxalate decarboxylase activity (molecular function)
metal ion binding (molecular function)
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