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Information on EC 2.8.3.16 - formyl-CoA transferase and Organism(s) Oxalobacter formigenes and UniProt Accession O06644
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2.8.3.16 formyl-CoA transferaseIUBMB Comments
The enzyme from Oxalobacter formigenes can also catalyse the transfer of CoA from formyl-CoA to succinate.
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Word Map
- 2.8.3.16
- medicine
- molecular biology
- environmental protection
- formigenes
- oxalobacter
- oxalyl-coa
-
oxalate-degrading
-
probiotic
-
stone
-
oxalyl-coenzyme
-
oxalyl
- hyperoxaluria
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urolithiasis
- acidophilus
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commensal
-
anhydride
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lactobacilli
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oxalate-dependent
The taxonomic range for the selected organisms is: Oxalobacter formigenes
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
formyl-coa transferase, formyl-coenzyme a transferase, formyl coenzyme a transferase, fcoct, formyl-coa:oxalate coa-transferase, formyl-coa-transferase, formyl-coa oxalate coa-transferase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
coenzyme A-transferase, formyl coenzyme A-oxalate
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-
-
-
formyl-CoA oxalate CoA-transferase
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-
-
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formyl-coenzyme A transferase
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-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
formyl-CoA + oxalate = formate + oxalyl-CoA
CoA binding sites are located at the interface between the subunits of the dimer
formyl-CoA + oxalate = formate + oxalyl-CoA
reaction mechanism, no classical ping-pong mechanism
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
coenzyme A transfer
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-
-
-
PATHWAY SOURCE
PATHWAYS
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-
SYSTEMATIC NAME
IUBMB Comments
formyl-CoA:oxalate CoA-transferase
The enzyme from Oxalobacter formigenes can also catalyse the transfer of CoA from formyl-CoA to succinate.
CAS REGISTRY NUMBER
COMMENTARY
128826-27-7
-
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
formyl-CoA + oxalate
formate + oxalyl-CoA
activation-decarboxylation reaction in the catabolism of oxalic acid, degradation and detoxification in mammalian intestinal flora
-
?
formyl-CoA + oxalate
formate + oxalyl-CoA
activation-decarboxylation reaction in the catabolism of oxalic acid, degradation and detoxification in mammalian intestinal flora
-
?
formyl-CoA + oxalate
formate + oxalyl-CoA
FRC and oxalyl-CoA decarboxylase are essential for the survival of Oxalobacter in that they mediate the conversion of oxalate into formate and CO2 in a coupled catalytic cycle
-
-
?
formyl-CoA + oxalate
formate + oxalyl-CoA
oxalate catabolism has a central role in Oxalobacter formigenes, where oxalate serves as vital source of energy as well as carbon
-
-
r
formyl-CoA + oxalate
formate + oxalyl-CoA
oxalate is a highly oxidized compound that may be used as C- and energy sources by oxalotrophic bacteria
-
-
?
formyl-CoA + oxalate
formate + oxalyl-CoA
catalytic mechanism, beta-aspartyl-CoA thioester as intermediate
-
-
r
succinyl-CoA + oxalate
succinate + oxalyl-CoA
no activity with the recombinant enzyme expressed in Escherichia coli
-
-
?
succinyl-CoA + oxalate
succinate + oxalyl-CoA
11% of the reaction rate observed with formyl-CoA
-
?
formyl-CoA + oxalate
formate + oxalyl-CoA
-
involvement of the Asp169 side chain in mediating enzyme-catalyzed CoA transfer via a series of anhydride intermediates
-
-
?
formyl-CoA + oxalate
formate + oxalyl-CoA
-
oxalyl-CoA decarboxylase and formyl-CoA transferase are the key enzymes in the oxalate catabolism of Oxalobacter formigenes which dwell in the intestine of vertebrates and have an important symbiotic relationship with their hosts
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-
?
additional information
?
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no activity with acetate or malonate
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-
?
additional information
?
-
-
no activity with acetate or malonate
-
-
?
additional information
?
-
no activity with acetate or malonate
-
-
?
additional information
?
-
-
no activity with acetate or malonate
-
-
?
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
formyl-CoA + oxalate
formate + oxalyl-CoA
-
oxalyl-CoA decarboxylase and formyl-CoA transferase are the key enzymes in the oxalate catabolism of Oxalobacter formigenes which dwell in the intestine of vertebrates and have an important symbiotic relationship with their hosts
-
-
?
formyl-CoA + oxalate
formate + oxalyl-CoA
activation-decarboxylation reaction in the catabolism of oxalic acid, degradation and detoxification in mammalian intestinal flora
-
?
formyl-CoA + oxalate
formate + oxalyl-CoA
activation-decarboxylation reaction in the catabolism of oxalic acid, degradation and detoxification in mammalian intestinal flora
-
?
formyl-CoA + oxalate
formate + oxalyl-CoA
FRC and oxalyl-CoA decarboxylase are essential for the survival of Oxalobacter in that they mediate the conversion of oxalate into formate and CO2 in a coupled catalytic cycle
-
-
?
formyl-CoA + oxalate
formate + oxalyl-CoA
oxalate catabolism has a central role in Oxalobacter formigenes, where oxalate serves as vital source of energy as well as carbon
-
-
r
formyl-CoA + oxalate
formate + oxalyl-CoA
oxalate is a highly oxidized compound that may be used as C- and energy sources by oxalotrophic bacteria
-
-
?
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
p-chloromercuribenzoate
91% inhibition at 1 mM, causes precipitation
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
74
oxalate
W48Q FRC, the W48F FRC is not inhibited by oxalate at concentrations of up to 154 mM
additional information
additional information
-
Kis for formate is 17 mM, Kii for formate is 380 mM, Kis for oxalyl-CoA is 0.15 mM, Kii for oxalyl-CoA is 0.28 mM
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
soil samples are collected below the Ca-oxalate producing trees Milicia excelsa and Afzelia africana and in a similar soil distant from trees
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
monomer
dimer
enzyme monomers are tightly interacting and are interlocked, three-dimensional crystal structure analysis
dimer
identified through crystallographic freeze-trapping experiments with formyl-CoA and oxalyl-CoA in the absence of acceptor carboxylic acid
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
beta-aspartyl-CoA thioester intermediate is identified by x-ray crystallography
FRC variants W48F and W48Q, hanging drop vapour diffusion method
purified recombinant enzyme from overexpression in Escherichia coli, hanging drop method, protein solution: 7.5 mg/ml, 25 mM MES, pH 6.2, 10% glycerol, drop volume 0.002 ml, reservoir solution: 100 mM HEPES, pH 7.5, 26% polyethylene glycol 4000, 0.5 M MgCl2, 291 K, 1 week, X-ray diffraction structure determination and analysis
purified recombinant selenocysteine-substituted enzyme, hanging drop method, protein solution: 4.75 mg/ml, 25 mM MES, pH 6.2, 10% glycerol, drop volume 0.002 ml, reservoir solution: 100 mM HEPES, pH 7.5, 26% polyethylene glycol 4000, 0.5 M MgCl2, 291 K, 2 weeks, X-ray diffraction structure determination and analysis
crystallization and structure determination of the enzyme/oxalyl-CoA complex, hanging drop technique. Crystallization and structure determination of the D169A, D169E, and D169S mutants
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D169A
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mutant enzyme is correctly folded and forms interlocked dimers, 1300fold decrease in activity
D169E
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mutant enzyme is correctly folded and forms interlocked dimers, inactive mutant enzyme
D169S
-
mutant enzyme is correctly folded and forms interlocked dimers, inactive mutant enzyme
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80°C, 25 mM sodium phosphate, pH 6.2, 300 mM NaCl, 1 mM dithiothreitol and 10% glycerol
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
DEAE anion exchange chromatography, Blue-Sepharose fast flow affinity chromatography, Sephadex G-250 size exclusion chromatography, and QHP anion exchange chromatography
His-tagged FRC protein is purified by Ni-nitrilotriacetic acid column and subsequent gel filtration
selenocysteine-substituted enzyme mutant, recombinant from Escherichia coli, to homogeneity
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
DNA sequence determination and analysis, monocistronic operon, overexpression in Escherichia coli, activity is similar to the wild-type enzyme
selenocysteine-substituted enzyme mutant, expression in Escherichia coli
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
environmental protection
bacterial oxalate-degrading function, microbiological processes are considered as the main oxalate sinks in natural environments, in soil oxalate from fungi, plant root exudates and decaying plant tissues display powerful metal chelating properties. Oxalate takes part in plant nutrition status by increasing the availability of phosphate and other poorly soluble micro-nutriments, through its ability to complex and remove excess metal cations. It also plays an important role in the detoxification of heavy metals in the vicinity of plant roots.
medicine
bacterial oxalate-degrading function, in humans an accumulation of oxalic acid can result in a number of pathologic conditions, including hyperoxaluria, urolithiasis, renal failure, cardiomyopathy and cardiac conductance disorders
molecular biology
use of the frc gene as template for PCR to detect oxalotrophic bacteria
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Baetz, A.L.; Allison, M.J.
Purification and characterization of formyl-coenzyme A transferase from Oxalobacter formigenes
J. Bacteriol.
172
3537-3540
1990
Oxalobacter formigenes (O06644), Oxalobacter formigenes
Baetz, A.L.; Allison, M.J.
Localization of oxalyl-coenzyme A decarboxylase, and formyl-coenzyme A transferase in Oxalobacter formigenes cells
Syst. Appl. Microbiol.
15
167-171
1992
Oxalobacter formigenes (O06644), Oxalobacter formigenes OxB / ATCC 35274 (O06644)
-
Sidhu, H.; Ogden, S.D.; Lung, H.Y.; Luttge, B.G.; Baetz, A.L.; Peck, A.B.
DNA sequencing and expression of the formyl coenzyme A transferase gene, frc, from, Oxalobacter formigenes
J. Bacteriol.
179
3378-3381
1997
Oxalobacter formigenes (O06644), Oxalobacter formigenes
Ricagno, S.; Jonsson, S.; Richards, N.; Lindqvist, Y.
Crystallization and preliminary crystallographic analysis of formyl-CoA tranferase from Oxalobacter formigenes
Acta Crystallogr. Sect. D
59
1276-1277
2003
Oxalobacter formigenes (O06644), Oxalobacter formigenes
Ricagno, S.; Jonsson, S.; Richards, N.; Lindqvist, Y.
Formyl-CoA transferase encloses the CoA binding site at the interface of an interlocked dimer
EMBO J.
22
3210-3219
2003
Oxalobacter formigenes (O06644), Oxalobacter formigenes
Jonsson, S.; Ricagno, S.; Lindqvist, Y.; Richards, N.G.
Kinetic and mechanistic characterization of the formyl-CoA transferase from Oxalobacter formigenes
J. Biol. Chem.
279
36003-36012
2004
Oxalobacter formigenes
Ye, Z.Q.; Kong, D.B.; Chen, Z.Q.; Yao, L.F.; Guo, H.; Yu, X.; Liu, G.L.; Yang, W.M.
Stable expression of the oxc and frc genes from Oxalobacter formigenes in human embryo kidney 293 cells: implications for gene therapy of hyperoxaluria
Int. J. Mol. Med.
20
521-526
2007
Oxalobacter formigenes
Toyota, C.G.; Berthold, C.L.; Gruez, A.; Jonsson, S.; Lindqvist, Y.; Cambillau, C.; Richards, N.G.
Differential substrate specificity and kinetic behavior of Escherichia coli YfdW and Oxalobacter formigenes formyl coenzyme A transferase
J. Bacteriol.
190
2556-2564
2008
Escherichia coli, Escherichia coli MG1655, Oxalobacter formigenes (O06644), Oxalobacter formigenes
Berthold, C.L.; Toyota, C.G.; Richards, N.G.; Lindqvist, Y.
Reinvestigation of the catalytic mechanism of formyl-CoA transferase, a class III CoA-transferase
J. Biol. Chem.
283
6519-6529
2008
Oxalobacter formigenes (O06644), Oxalobacter formigenes
Khammar, N.; Martin, G.; Ferro, K.; Job, D.; Aragno, M.; Verrecchia, E.
Use of the frc gene as a molecular marker to characterize oxalate-oxidizing bacterial abundance and diversity structure in soil
J. Microbiol. Methods
76
120-127
2008
Streptomyces violaceoruber, Variovorax paradoxus, Azospirillum brasilense, Azospirillum lipoferum, Escherichia coli, Escherichia coli (P69902), Methylorubrum extorquens, Methylobacterium organophilum, Cupriavidus oxalaticus, Starkeya novella, Xanthobacter flavus, Xanthomonas sp., Ancylobacter oerskovii, Methylorubrum thiocyanatum, Pandoraea sp., Oxalicibacterium flavum, Arquibacter sp., Herminiimonas saxobsidens, Azorhizobium sp., Herminiimonas arsenicoxydans (A4G241), Herminiimonas arsenicoxydans (A4G242), Bradyrhizobium sp. (A5EGD7), Janthinobacterium sp. Marseille (A6T0J2), Xanthobacter autotrophicus (A7ICK2), Ancylobacter polymorphus (B3VMH8), Oxalobacter formigenes (O06644), Streptomyces coelicolor (O87838), Shigella flexneri (P69903), Cupriavidus necator (Q0K0H8), Cupriavidus necator (Q46S66), Cupriavidus necator (Q46S72), Paraburkholderia xenovorans (Q13RQ4), Rhodopseudomonas palustris (Q6N8F8), Streptomyces avermitilis (Q82M40), Bradyrhizobium japonicum (Q89QH2), Cupriavidus necator JMP 134-1 (Q46S72)
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