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Literature summary extracted from

  • Just, V.J.; Burrell, M.R.; Bowater, L.; McRobbie, I.; Stevenson, C.E.; Lawson, D.M.; Bornemann, S.
    The identity of the active site of oxalate decarboxylase and the importance of the stability of active-site lid conformations (2007), Biochem. J., 407, 397-406.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
4.1.1.2 gene oxdC, expression of the C-terminally His6-tagged protein in Escherichia coli strain BL21(DE3) Bacillus subtilis

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
4.1.1.2 purified recombinant mutants R92A, DELTA162-163, S161A, and E162A, hanging-drop vapour diffusion method at 18°C, the mutants enzymes generally crystallize with 8-15% v/v PEG 8000, 0.1 M Tris, pH 8.5, and 0-15% xylitol, further method optimization for each mutant enzyme, X-ray diffraction structure determination and analysis at 2.0-3.1 A resolution, molecular modelling Bacillus subtilis

Protein Variants

EC Number Protein Variants Comment Organism
4.1.1.2 D297A site-directed mutagenesis, the mutant shows reduced activity and altered kinetics compared to the wild-type enzyme Bacillus subtilis
4.1.1.2 E162A site-directed mutagenesis, the mutant lacks both oxalate decarboxylase and oxalate oxidase activities, structure analysis Bacillus subtilis
4.1.1.2 E162D site-directed mutagenesis, E162D mutant retains 29% of the decarboxylase activity compared to the wild-type enzyme Bacillus subtilis
4.1.1.2 E162Q site-directed mutagenesis, E162Q mutant retains only 1% of the decarboxylase activity compared to the wild-type enzyme Bacillus subtilis
4.1.1.2 E333A site-directed mutagenesis, the mutant shows reduced oxalate decarboxylase and oxalate oxidase activities compared to the wild-type enzyme Bacillus subtilis
4.1.1.2 E333Q site-directed mutagenesis, the mutant lacks both oxalate decarboxylase and oxalate oxidase activities Bacillus subtilis
4.1.1.2 E33D site-directed mutagenesis, the mutant shows reduced activity and altered kinetics compared to the wild-type enzyme Bacillus subtilis
4.1.1.2 H299A site-directed mutagenesis, the mutant shows reduced activity and altered kinetics compared to the wild-type enzyme Bacillus subtilis
4.1.1.2 additional information construction of deletion mutant DELTA162-163 or inactive deletion mutant DELTA162-164, structure analysis, manganese content of mutant enzymes, overview Bacillus subtilis
4.1.1.2 R270A site-directed mutagenesis, the mutant shows altered kinetics compared to the wild-type enzyme Bacillus subtilis
4.1.1.2 R270Q site-directed mutagenesis, the mutant shows altered kinetics compared to the wild-type enzyme Bacillus subtilis
4.1.1.2 R92A site-directed mutagenesis, the mutant lacks both oxalate decarboxylase and oxalate oxidase activities, structure analysis Bacillus subtilis
4.1.1.2 R92K site-directed mutagenesis, the mutant lacks both oxalate decarboxylase and oxalate oxidase activities Bacillus subtilis
4.1.1.2 S161A site-directed mutagenesis, the mutant shows reduced activity and altered kinetics compared to the wild-type enzyme, structure analysis Bacillus subtilis
4.1.1.2 S164A site-directed mutagenesis, the mutant shows reduced activity and altered kinetics compared to the wild-type enzyme Bacillus subtilis
4.1.1.2 T165P site-directed mutagenesis, altered comformation with dominant conformation of the lid compared to the wild-type enzyme Bacillus subtilis

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
4.1.1.2 additional information
-
 additional information kinetic analysis, different assay methods Bacillus subtilis
4.1.1.2 1.14
-
 oxalate pH 4.0, 26°C, recombinant mutant R270Q Bacillus subtilis
4.1.1.2 1.9
-
 oxalate pH 4.0, 26°C, recombinant mutant R92K Bacillus subtilis
4.1.1.2 2.3
-
 oxalate pH 4.0, 26°C, recombinant deletion mutant DELTA163-163 Bacillus subtilis
4.1.1.2 4.1
-
 oxalate pH 4.0, 26°C, recombinant mutant E333A Bacillus subtilis
4.1.1.2 6.3
-
 oxalate pH 4.0, 26°C, recombinant mutant E333D Bacillus subtilis
4.1.1.2 6.6 16.4 oxalate pH 4.0, 26°C, recombinant wild-type enzyme Bacillus subtilis
4.1.1.2 8
-
 oxalate pH 4.0, 26°C, recombinant mutant R270A Bacillus subtilis
4.1.1.2 11.2
-
 oxalate pH 4.0, 26°C, recombinant mutant D297A Bacillus subtilis
4.1.1.2 11.6
-
 oxalate pH 4.0, 26°C, recombinant mutant H299A Bacillus subtilis
4.1.1.2 13.5
-
 oxalate pH 4.0, 26°C, recombinant mutant E162Q Bacillus subtilis
4.1.1.2 17.4
-
 oxalate pH 4.0, 26°C, recombinant mutant E162D Bacillus subtilis
4.1.1.2 25
-
 oxalate pH 4.0, 26°C, recombinant mutant T165P Bacillus subtilis
4.1.1.2 31
-
 oxalate pH 4.0, 26°C, recombinant mutant S164A Bacillus subtilis
4.1.1.2 71
-
 oxalate pH 4.0, 26°C, recombinant mutant E161A Bacillus subtilis

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
4.1.1.2 Mn2+ required, each subunit contains two similar, but distinct, manganese sites 1 and 2, only site 1 is catalytically active, and site 2 is purely structural, manganese content of mutant enzymes, overview Bacillus subtilis
4.1.1.2 O2 required for catalysis Bacillus subtilis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
4.1.1.2 oxalate + H+ Bacillus subtilis
-
 formate + CO2
-
 ir
4.1.1.2 oxalate + H+ Bacillus subtilis 168
-
 formate + CO2
-
 ir

Organism

EC Number Organism UniProt Comment Textmining
4.1.1.2 Bacillus subtilis O34714 gene oxdC
-
4.1.1.2 Bacillus subtilis 168 O34714 gene oxdC
-

Purification (Commentary)

EC Number Purification (Comment) Organism
4.1.1.2 recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration Bacillus subtilis

Specific Activity [micromol/min/mg]

EC Number Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
4.1.1.2 additional information
-
 activity of recombinant wild-type and mutant enzymes, overview Bacillus subtilis

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.1.1.2 additional information the enzyme also shows oxalate oxidase activity, catalytic cycle, overview Bacillus subtilis ?
-
 ?
4.1.1.2 additional information the enzyme also shows oxalate oxidase activity, catalytic cycle, overview Bacillus subtilis 168 ?
-
 ?
4.1.1.2 oxalate + H+
-
 Bacillus subtilis formate + CO2
-
 ir
4.1.1.2 oxalate + H+ catalytic cycle involving radical formation with O2, overview, only Mn2+ binding site 1 is catalytically active, while Mn2+ binding site 2 is purely structural, overview Bacillus subtilis formate + CO2
-
 ir
4.1.1.2 oxalate + H+
-
 Bacillus subtilis 168 formate + CO2
-
 ir
4.1.1.2 oxalate + H+ catalytic cycle involving radical formation with O2, overview, only Mn2+ binding site 1 is catalytically active, while Mn2+ binding site 2 is purely structural, overview Bacillus subtilis 168 formate + CO2
-
 ir

Subunits

EC Number Subunits Comment Organism
4.1.1.2 hexamer homohexamer, each subunit contains two similar, but distinct, manganese sites, only site 1 is catalytically active and site 2 is purely structural Bacillus subtilis

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
4.1.1.2 26
-
 assay at Bacillus subtilis

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
4.1.1.2 4
-
 assay at Bacillus subtilis