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Information on EC 4.1.1.8 - oxalyl-CoA decarboxylase and Organism(s) Oxalobacter formigenes and UniProt Accession P40149

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EC Tree
     4 Lyases
         4.1 Carbon-carbon lyases
             4.1.1 Carboxy-lyases
                4.1.1.8 oxalyl-CoA decarboxylase
IUBMB Comments
A thiamine-diphosphate protein.
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This record set is specific for:
Oxalobacter formigenes
UNIPROT: P40149
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Word Map
The taxonomic range for the selected organisms is: Oxalobacter formigenes
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Reaction Schemes
Synonyms
oxalyl-coa decarboxylase, oxalyl-coenzyme a decarboxylase, oxalyl coa decarboxylase, oxalyl coenzyme a decarboxylase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Oxalyl coenzyme A decarboxylase
-
Decarboxylase, oxalyl coenzyme A
-
-
-
-
Oxalyl coenzyme A decarboxylase
-
-
-
-
oxalyl-coenzyme A decarboxylase
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
decarboxylation
-
-
-
-
PATHWAY SOURCE
PATHWAYS
-
-, -, -
SYSTEMATIC NAME
IUBMB Comments
oxalyl-CoA carboxy-lyase (formyl-CoA-forming)
A thiamine-diphosphate protein.
CAS REGISTRY NUMBER
COMMENTARY hide
9024-96-8
-
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
Formyl-CoA + CO2
show the reaction diagram
-
-
-
?
Oxalyl-CoA
Formyl-CoA + CO2
show the reaction diagram
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
Oxalyl-CoA
Formyl-CoA + CO2
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
thiamine diphosphate
required
thiamine diphosphate
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
-
activates
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3-deazathiamine diphosphate
efficient inhibitor
CoA
-
mixed inhibitor with respect to oxalyl-CoA
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ADP
-
stimulates
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.018 - 0.066
oxalyl-CoA
0.023 - 0.24
oxalyl-CoA
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.1 - 88
oxalyl-CoA
88
oxalyl-CoA
-
pH 6.7, 30°C
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.4
CoA
-
pH 6.7, 30°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.7
-
oxalyl-CoA
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
-
the commensal bacterium Oxalobacter formigenes consumes oxalate by converting it to oxalyl-CoA, which is decarboxylated by oxalyl-CoA decarboxylase
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
OXC_OXAFO
568
0
60684
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
243000
-
gel filtration
65000
-
4 * 65000, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
tetramer
x-ray crystallography
tetramer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
-
PROTEIN VARIANTS
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
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Blue-sepharose column chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
expressed in Escherichia coli
-
expression in Escherichia coli
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
-
gene transfer to human cells for urolithiasis therapy, considered
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Baetz, A.L.; Allison, M.J.
Purification and characterization of oxalyl-coenzyme A decarboxylase from Oxalobacter formigenes
J. Bacteriol.
171
2605-2608
1989
Oxalobacter formigenes
Manually annotated by BRENDA team
Lung, H.Y.; Cornelius, J.G.; Peck, A.B.
Cloning and expression of the Oxalyl-CoA decarboxylase gene from the bacterium, Oxalobacter formigenes: Prospects for gene therapy to control Ca-Oxalate kidney stone formation
Am. J. Kidney Dis.
17
381-385
1991
Oxalobacter formigenes
Manually annotated by BRENDA team
Lung, H.Y.; Baetz, A.L.; Peck, A.B.
Molecular cloning, DNA sequence, and gene expression of the oxalyl-coenzyme A decarboxylase gene, oxc, from the bacterium Oxalobacter formigenes
J. Bacteriol.
176
2468-2472
1994
Oxalobacter formigenes
Manually annotated by BRENDA team
Berthold, C.L.; Sidhu, H.; Ricagno, S.; Richards, N.G.; Lindqvist, Y.
Detection and characterization of merohedral twinning in crystals of oxalyl-coenzyme A decarboxylase from Oxalobacter formigenes
Biochim. Biophys. Acta
1764
122-128
2006
Oxalobacter formigenes
Manually annotated by BRENDA team
Berthold, C.L.; Moussatche, P.; Richards, N.G.; Lindqvist, Y.
Structural basis for activation of the thiamin diphosphate-dependent enzyme oxalyl-CoA decarboxylase by adenosine diphosphate
J. Biol. Chem.
280
41645-41654
2005
Oxalobacter formigenes
Manually annotated by BRENDA team
Bendazzoli, C.; Turroni, S.; Gotti, R.; Olmo, S.; Brigidi, P.; Cavrini, V.
Determination of oxalyl-coenzyme A decarboxylase activity in Oxalobacter formigenes and Lactobacillus acidophilus by capillary electrophoresis
J. Chromatogr. B
854
350-356
2007
Lactobacillus acidophilus, Lactobacillus acidophilus LA 14, Oxalobacter formigenes
Manually annotated by BRENDA team
Berthold, C.L.; Toyota, C.G.; Moussatche, P.; Wood, M.D.; Leeper, F.; Richards, N.G.; Lindqvist, Y.
Crystallographic snapshots of oxalyl-CoA decarboxylase give insights into catalysis by nonoxidative ThDP-dependent decarboxylases
Structure
15
853-861
2007
Oxalobacter formigenes (P40149)
Manually annotated by BRENDA team
Abratt, V.R.; Reid, S.J.
Oxalate-degrading bacteria of the human gut as probiotics in the management of kidney stone disease
Adv. Appl. Microbiol.
72
63-87
2010
Bifidobacterium animalis subsp. lactis, Bifidobacterium dentium, Bifidobacterium dentium ATCC 27678, Bifidobacterium gallicum (D1NS77), Bifidobacterium gallicum DSM 20093 (D1NS77), Bradyrhizobium japonicum ORS278 (A4YXN1), Bradyrhizobium sp. (A4YXN1), Eggerthella lenta, Enterococcus faecalis, Escherichia coli, Escherichia coli ATCC 8739, Lactobacillus acidophilus (A4PE17), Lactobacillus acidophilus ATCC 4796 (A4PE17), Lactobacillus gasseri, Lactobacillus gasseri Gasser AM63, Lactobacillus johnsonii (C2E3B5), Lactobacillus johnsonii ATCC 33200 (C2E3B5), Limosilactobacillus reuteri, Limosilactobacillus reuteri 100-23, Oxalobacter formigenes (C3XBB9), Oxalobacter formigenes, Oxalobacter formigenes OXCC13 (C3XBB9), Paraburkholderia phytofirmans (B2T9D2), Paraburkholderia phytofirmans PsJN (B2T9D2), Providencia rettgeri (D4C4C5), Providencia rettgeri DSM 1131 (D4C4C5), Shigella boydii (Q31Y98), Shigella boydii Sb 227 (Q31Y98)
Manually annotated by BRENDA team
Mullins, E.A.; Sullivan, K.L.; Kappock, T.J.
Function and X-ray crystal structure of Escherichia coli YfdE
PLoS ONE
8
e67901
2013
Escherichia coli, Oxalobacter formigenes
Manually annotated by BRENDA team