Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 44223.16 
• Atom Count: 2976 
• Residue Count: 385 
• Unique protein chains: 1

1J58

Crystal Structure of Oxalate Decarboxylase

• DOI: 10.2210/pdb1J58/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Bacillus subtilis (strain 168)
• Expression System: Bacteria


• Deposited: 2002-02-25 Released: 2002-07-03 
• Deposition Author(s): Anand, R., Dorrestein, P.C., Kinsland, C., Begley, T.P., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.197 
• R-Value Work: 0.176 

Literature

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: 7659-7669

• PubMed: 12056897 
• Primary Citation of Related Structures:  
  1L3J
• Also Cited By: 1UW8


• PubMed Abstract: 
  

Oxalate decarboxylase is a manganese-dependent enzyme that catalyzes the conversion of oxalate to formate and carbon dioxide. We have determined the structure of oxalate decarboxylase from Bacillus subtilis at 1.75 A resolution in the presence of formate. The structure reveals a hexamer with 32-point symmetry in which each monomer belongs to the cupin family of proteins. Oxalate decarboxylase is further classified as a bicupin because it contains two cupin folds, possibly resulting from gene duplication. Each oxalate decarboxylase cupin domain contains one manganese binding site. Each of the oxalate decarboxylase domains is structurally similar to oxalate oxidase, which catalyzes the manganese-dependent oxidative decarboxylation of oxalate to carbon dioxide and hydrogen peroxide. Amino acid side chains in the two metal binding sites of oxalate decarboxylase and the metal binding site of oxalate oxidase are very similar. Four manganese binding residues (three histidines and one glutamate) are conserved as well as a number of hydrophobic residues. The most notable difference is the presence of Glu333 in the metal binding site of the second cupin domain of oxalate decarboxylase. We postulate that this domain is responsible for the decarboxylase activity and that Glu333 serves as a proton donor in the production of formate. Mutation of Glu333 to alanine reduces the catalytic activity by a factor of 25. The function of the other domain in oxalate decarboxylase is not yet known.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
YVRK PROTEIN	A	385	Bacillus subtilis (strain 168)	Mutation(s): 0  Gene Names: oxdC (yvrK) EC: 4.1.1.2
Find proteins for O34714 (Bacillus subtilis (strain 168)) Go to UniProtKB:  O34714

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MN	A	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
FMT	A	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.197 
• R-Value Work: 0.176 
• Space Group: H 3 2

Unit Cell:

Length (Å)	Angle (°)
a = 154.700	α = 90.00
b = 154.700	β = 90.00
c = 123.700	γ = 120.00

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-02-25 
• Released Date: 2002-07-03 
• Deposition Author(s): Anand, R., Dorrestein, P.C., Kinsland, C., Begley, T.P., Ealick, S.E.

Revision History 

• Version 1.0: 2002-07-03
  Type: Initial release
• Version 1.1: 2008-04-26
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Derived calculations, Version format compliance