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Information on EC 4.1.1.8 - oxalyl-CoA decarboxylase and Organism(s) Escherichia coli and UniProt Accession P0AFI0
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4.1.1.8 oxalyl-CoA decarboxylaseIUBMB Comments
A thiamine-diphosphate protein.
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Word Map
- 4.1.1.8
- oxalate
- oxalobacter
- formigenes
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oxalate-degrading
- stone
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urolithiasis
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probiotic
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hyperoxaluria
- lactobacillus
- thiamin
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formyl-coenzyme
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fecal
- bifidobacterium
- acidophilus
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diphosphate-dependent
- medicine
The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Synonyms
oxalyl-coa decarboxylase, oxalyl-coenzyme a decarboxylase, oxalyl coa decarboxylase, oxalyl coenzyme a decarboxylase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Decarboxylase, oxalyl coenzyme A
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Oxalyl coenzyme A decarboxylase
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
decarboxylation
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SYSTEMATIC NAME
IUBMB Comments
oxalyl-CoA carboxy-lyase (formyl-CoA-forming)
A thiamine-diphosphate protein.
CAS REGISTRY NUMBER
COMMENTARY
9024-96-8
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ADP
the presence of 0.3 mM ADP results in a marginal increase in kcat and a small decrease in Km, leading to a 1.7fold higher catalytic efficiency. One molecule of ADP is bound per monomer distant from the CoA binding site
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
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
physiological function
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proteins YfdW and YfdU are necessary and sufficient for oxalate-induced protection against a subsequent acid challenge. EvgA activates proton-consuming amino acid decarboxylases during strong acid resistance responses. Oxalate catabolism counteracts acid stress by oxalyl-CoA decarboxylation. Oxalate elicits a moderate, rpoS-independent acid tolerance response that requires both yfdW and yfdU in Escherichia coli. But product(s) of the yfdXWUVE operon appear to have no essential role in general acid stress responses and may serve a more specialized function
physiological function
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the enzymes YfdW, a formyl coenzyme A (CoA) transferase, and YfdU, an oxalyl-CoA decarboxylase, are required for oxalate adaptation but not during challenge in minimal challenge medium. YfdW and YfdU are part of an AR2-like system where oxalate is brought into the cell by YhjX and decarboxylated in a reaction similar to that catalyzed by GadA/B in the challenge medium. Oxalate induces an acid tolerance response when Escherichia coli cells are adapted at pH 5.5 and the enzymes YfdW and YfdU, but not YhjX, are required for this response, overview
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
streptomycin sulfate precipitation, ammonium sulfate precipitation, Q-Sepharose column chromatography, and Superdex 200 gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
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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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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)
Werther, T.; Zimmer, A.; Wille, G.; Golbik, R.; Weiss, M.S.; Koenig, S.
New insights into structure-function relationships of oxalyl CoA decarboxylase from Escherichia coli
FEBS J.
277
2628-2640
2010
Escherichia coli (P0AFI0), Escherichia coli
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
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