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CRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.129 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A Closed Conformation of Bacillus Subtilis Oxalate Decarboxylase Oxdc Provides Evidence for the True Identity of the Active Site

Just, V.J.Stevenson, C.E.M.Bowater, L.Tanner, A.Lawson, D.M.Bornemann, S.

(2004) J Biol Chem 279: 19867

  • DOI: 10.1074/jbc.M313820200
  • Primary Citation of Related Structures:  
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  • PubMed Abstract: 
  • Oxalate decarboxylase (EC 4.1.1.2) catalyzes the conversion of oxalate to formate and carbon dioxide and utilizes dioxygen as a cofactor. By contrast, the evolutionarily related oxalate oxidase (EC 1.2.3.4) converts oxalate and dioxygen to carbon dioxide and hydrogen peroxide ...

    Oxalate decarboxylase (EC 4.1.1.2) catalyzes the conversion of oxalate to formate and carbon dioxide and utilizes dioxygen as a cofactor. By contrast, the evolutionarily related oxalate oxidase (EC 1.2.3.4) converts oxalate and dioxygen to carbon dioxide and hydrogen peroxide. Divergent free radical catalytic mechanisms have been proposed for these enzymes that involve the requirement of an active site proton donor in the decarboxylase but not the oxidase reaction. The oxidase possesses only one domain and manganese binding site per subunit, while the decarboxylase has two domains and two manganese sites per subunit. A structure of the decarboxylase together with a limited mutagenesis study has recently been interpreted as evidence that the C-terminal domain manganese binding site (site 2) is the catalytic site and that Glu-333 is the crucial proton donor (Anand, R., Dorrestein, P. C., Kinsland, C., Begley, T. P., and Ealick, S. E. (2002) Biochemistry 41, 7659-7669). The N-terminal binding site (site 1) of this structure is solvent-exposed (open) and lacks a suitable proton donor for the decarboxylase reaction. We report a new structure of the decarboxylase that shows a loop containing a 3(10) helix near site 1 in an alternative conformation. This loop adopts a "closed" conformation forming a lid covering the entrance to site 1. This conformational change brings Glu-162 close to the manganese ion, making it a new candidate for the crucial proton donor. Site-directed mutagenesis of equivalent residues in each domain provides evidence that Glu-162 performs this vital role and that the N-terminal domain is either the sole or the dominant catalytically active domain.


    Related Citations: 
    • Structure of Oxalate Decarboxylase from Bacillus Subtilis at 1.75 A Resolution
      Anand, R., Dorrestein, P.C., Kinsland, C., Begley, T.P., Ealick, S.E.
      (2002) Biochemistry 41: 7659
    • Oxalate Decarboxylase Requires Manganese and Dioxygen for Activity
      Tanner, A., Bowater, L., Fairhurst, S.A., Bornemann, S.
      (2001) J Biol Chem 276: 43627

    Organizational Affiliation

    Biological Chemistry Department, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
OXALATE DECARBOXYLASE OXDCA385Bacillus subtilisMutation(s): 0 
EC: 4.1.1.2
Find proteins for O34714 (Bacillus subtilis (strain 168))
Explore O34714 
Go to UniProtKB:  O34714
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
D [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.129 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.663α = 90
b = 154.663β = 90
c = 122.822γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-12
    Changes: Data collection
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation