Information on EC 4.1.1.8 - oxalyl-CoA decarboxylase

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota

EC NUMBER
COMMENTARY hide
4.1.1.8
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RECOMMENDED NAME
GeneOntology No.
oxalyl-CoA decarboxylase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
oxalyl-CoA = formyl-CoA + CO2
show the reaction diagram
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-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
decarboxylation
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Glyoxylate and dicarboxylate metabolism
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Metabolic pathways
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oxalate degradation II
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oxalate degradation III
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SYSTEMATIC NAME
IUBMB Comments
oxalyl-CoA carboxy-lyase (formyl-CoA-forming)
A thiamine-diphosphate protein.
CAS REGISTRY NUMBER
COMMENTARY hide
9024-96-8
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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Manually annotated by BRENDA team
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B1SAD1
UniProt
Manually annotated by BRENDA team
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B1SAD1
UniProt
Manually annotated by BRENDA team
pumpkin
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-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
strain LA 14
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-
Manually annotated by BRENDA team
strain LA14
EMBL
Manually annotated by BRENDA team
no activity in Bifidobacterium adolescentis
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Manually annotated by BRENDA team
no activity in Bifidobacterium adolescentis ATCC 15703
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-
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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UniProt
Manually annotated by BRENDA team
wheat
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-
Manually annotated by BRENDA team
bean
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-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
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the absence of the YfdU protein increases the cell vulnerability to low pH, oxalic acid, or both. Oxalate-dependent pH tolerance of the yfdU-deletion strain is clearly impaired, glutamate-dependent acid resistance is not impaired by deletion of the either yfdW or yfdU
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
Oxalyl-CoA
?
show the reaction diagram
Oxalyl-CoA
Formyl-CoA + CO2
show the reaction diagram
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
Oxalyl-CoA
?
show the reaction diagram
Oxalyl-CoA
Formyl-CoA + CO2
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
thiamine diphosphate
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mn2+
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activates
Zn2+
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activates
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3-deazathiamine diphosphate
efficient inhibitor
acetyl coenzyme A
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CoA
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mixed inhibitor with respect to oxalyl-CoA
p-chloromercuribenzene sulfonate
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
AMP
weak activating effect
ATP
weak activating effect
CHWPR
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enhances transcription activity in combination with retinoic acid receptor-related orphan receptor gamma and cofactor required for SP1 transcriptional activation unit 70
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additional information
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the enzyme production is strongly dependent on culture medium, requiring poor nutritional environment and repeated subculturing in order to maintain oxalate-degrading activity
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0048 - 1
oxalyl-CoA
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.1 - 88
oxalyl-CoA
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
12.6
oxalyl-CoA
Escherichia coli
P0AFI0
at pH 6.5 and 30C
1538
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.4
CoA
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pH 6.7, 30C
0.08
coenzyme A
at pH 6.5 and 30C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.6
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oxalyl-CoA
6.7
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oxalyl-CoA
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
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whole-cell degrades oxalate while the cell-free culture supernatant does not
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
60581
4 * 60581, calculated from amino acid sequence
63710
B9X297, C6AFP4
x * 63710, calculated from amino acid sequence; x * 63710, calculated from amino acid sequence
230000
small-angle X-ray solution scattering
243000
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homotetramer
4 * 60581, calculated from amino acid sequence
tetramer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ODC alone or in complex with either ADP or acetyl CoA, hanging drop vapor diffusion method, using 100 mM MES/NaOH, pH 6.5 and 1.5 M ammonium sulfate for ODC alone, or 100 mM MES/NaOH, pH 6.25 and 1.75 M ammonium sulfate for ADPbound ODC, or 100 mM MES/NaOH, pH 6.0, 0.2 M sodium acetate and 5% (w/v) poly(ethylene glycol) 4000 for acetyl CoA-bound ODC
cocrystallization of wild-type OXC with 1 mM CoA, with a precipitating solution containing 0.5 M CaCl2, 0.1 M BisTris propane (2-[bis(2-hydroxyethyl)amino]-2-(hydroxymethyl) propane-1,3-diol), pH 6.5, and 26% polyethylene glycol 550 monomethyl ether
recombinant, hanging drop vapour-diffusion method, native and seleno-methionine labelled enzyme is crystallized in two different conditions resulting in two different crystal forms, one showing poor diffraction and the other merohedral twinning. Crystals in the former category belong to the tetragonal space group P4(2)2(1)2, crystals in the latter category are obtained by cocrystallization of the protein with coenzyme A, thiamine diphosphate and Mg2+. The crystal is heavily twinned with a twin ratio of 0.43
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recombinant, hanging-drop vapour-diffusion method
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
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complete inactivation after 5 min
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-14C, sodium citrate buffer, pH 5.5, 2 months, 50% loss of activity
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-80 C, 25% glycerol, conditions for storing oxalate-degrading organisms without loss of activity
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3C, sodium citrate buffer, pH 5.5, 1 month, 60% loss of activity
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Blue-sepharose column chromatography
streptomycin sulfate precipitation, ammonium sulfate precipitation, Q-Sepharose column chromatography, and Superdex 200 gel filtration
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
expressed in Escherichia coli BL21 cells
expressed in Escherichia coli BL21(DE3) cells
expression in Escherichia coli
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gene yfdU
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overexpression in Escherichia coli as a T7-Oxc fusion protein
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
transcription of the yfdXWUVE operon containing yfdU, which encodes the enzyme, is activated by the acid-response regulator EvgA
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E121A
0.1% activity compared to the wild type enzyme
E121Q
3.8% activity compared to the wild type enzyme
E56A
no activity, mutant elutes with a retention time corresponding to that of a dimer
R555A
96% activity compared to the wild type enzyme
S553A
15% activity compared to the wild type enzyme
Y120A
0.3% activity compared to the wild type enzyme
Y120F
8.2% activity compared to the wild type enzyme
Y483A
1.6% activity compared to the wild type enzyme
Y483F
1.9% activity compared to the wild type enzyme
additional information
deletion mutant DELTA553-565 shows almost no activity
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
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gene transfer to human cells for urolithiasis therapy, considered
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