Oxalyl-CoA (ECMDB20182) (M2MDB001028)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (20)
Record Information
Version2.0
Creation Date2012-05-31 14:31:51 -0600
Update Date2015-06-03 17:19:28 -0600
Secondary Accession Numbers
  • ECMDB20182
Identification
Name:Oxalyl-CoA
DescriptionOxalyl-CoA is a member of the chemical class known as Coenzyme A and Derivatives. These are derivative of vitamin B5 containing a 4'-phosphopantetheine moiety attached to a diphospho-adenosine. Oxalyl CoA is invovled in the catabolism of toxic compound oxalate. Oxalyl coenzyme A (CoA) decarboxylase (Oxc) is a key enzyme in the catabolism of the highly toxic compound oxalate, catalyzing the decarboxylation of oxalyl-CoA to formyl-CoA. (PMID 15345383) Oxalyl-coenzyme A decarboxylase is a thiamin diphosphate dependent enzyme active in the catabolism of the highly toxic compound oxalate. (PMID 16198641)
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • CoA-oxalate
  • CoA-oxalic acid
  • Oxalyl-coenzyme a
Chemical Formula:C23H36N7O19P3S
Weight:Average: 839.554
Monoisotopic: 839.099952231
InChI Key:QVXMZFTWJVBUHP-IBOSZNHHSA-N
InChI:InChI=1S/C23H36N7O19P3S/c1-23(2,16(33)19(34)26-4-3-12(31)25-5-6-53-22(37)21(35)36)8-46-52(43,44)49-51(41,42)45-7-11-15(48-50(38,39)40)14(32)20(47-11)30-10-29-13-17(24)27-9-28-18(13)30/h9-11,14-16,20,32-33H,3-8H2,1-2H3,(H,25,31)(H,26,34)(H,35,36)(H,41,42)(H,43,44)(H2,24,27,28)(H2,38,39,40)/t11-,14-,15-,16+,20-/m1/s1
CAS number:Not Available
IUPAC Name:2-({2-[(3-{[(2R)-4-({[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-1,2-dihydroxy-3,3-dimethylbutylidene]amino}-1-hydroxypropylidene)amino]ethyl}sulfanyl)-2-oxoacetic acid
Traditional IUPAC Name:({2-[(3-{[(2R)-4-[({[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,2-dihydroxy-3,3-dimethylbutylidene]amino}-1-hydroxypropylidene)amino]ethyl}sulfanyl)(oxo)acetic acid
SMILES:[H][C@](O)(C(O)=NCCC(O)=NCCSC(=O)C(O)=O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@@]1([H])O[C@@]([H])(N2C=NC3=C(N)N=CN=C23)[C@]([H])(O)[C@]1([H])OP(O)(O)=O
Chemical Taxonomy
Description belongs to the class of inorganic compounds known as homogeneous other non-metal compounds. These are inorganic non-metallic compounds in which the largest atom belongs to the class of 'other non-metals'.
KingdomInorganic compounds
Super ClassHomogeneous non-metal compounds
ClassHomogeneous other non-metal compounds
Sub ClassNot Available
Direct ParentHomogeneous other non-metal compounds
Alternative ParentsNot Available
Substituents
  • Homogeneous other non metal
Molecular FrameworkNot Available
External Descriptors
Physical Properties
State:Not Available
Charge:-4
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility5.54 g/LALOGPS
logP-0.42ALOGPS
logP-4.1ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)0.81ChemAxon
pKa (Strongest Basic)4.8ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count21ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area407.91 ŲChemAxon
Rotatable Bond Count21ChemAxon
Refractivity175.05 m³·mol⁻¹ChemAxon
Polarizability72.11 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Hydrogen ion + Oxalyl-CoA <> Carbon dioxide + Formyl-CoA
Formyl-CoA + Oxalic acid <> Formic acid + Oxalyl-CoA
Oxalyl-CoA <> Formyl-CoA + Carbon dioxide
Hydrogen ion + Oxalyl-CoA Carbon dioxide + Formyl-CoA
Formyl-CoA + Oxalic acid Formic acid + Oxalyl-CoA
Formyl-CoA + Oxalic acid > Formic acid + Oxalyl-CoA
Oxalyl-CoA > Formyl-CoA + Carbon dioxide
Acetyl-CoA + Oxalic acid <> Acetic acid + Oxalyl-CoA
SMPDB Pathways:Not Available
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00ks-0931000110-22ded9fe531730449923View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000j-0911000000-19e3e76082c9e7682f2cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00ks-1920000000-2d4244f1d0638760c091View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0040-4930142370-1fa4f6902014b005941cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-3910200000-c7b620c7bb31afb999d7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-057i-5900100000-c407c65037998edc22bcView in MoNA
MSMass Spectrum (Electron Ionization)Not AvailableView in JSpectraViewer
References
References:
  • Berthold, C. L., Sidhu, H., Ricagno, S., Richards, N. G., Lindqvist, Y. (2006). "Detection and characterization of merohedral twinning in crystals of oxalyl-coenzyme A decarboxylase from Oxalobacter formigenes." Biochim Biophys Acta 1764:122-128. Pubmed: 16198641
  • Federici, F., Vitali, B., Gotti, R., Pasca, M. R., Gobbi, S., Peck, A. B., Brigidi, P. (2004). "Characterization and heterologous expression of the oxalyl coenzyme A decarboxylase gene from Bifidobacterium lactis." Appl Environ Microbiol 70:5066-5073. Pubmed: 15345383
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID15535
HMDB IDNot Available
Pubchem Compound ID439206
Kegg IDC00313
ChemSpider ID388346
Wikipedia IDNot Available
BioCyc IDOXALYL-COA
EcoCyc IDOXALYL-COA
Ligand ExpoOXK

Enzymes

Protein Details
1. Probable oxalyl-CoA decarboxylase
General function:
Involved in oxalyl-CoA decarboxylase activity
Specific function:
Oxalyl-CoA = formyl-CoA + CO(2)
Gene Name:
oxc
Uniprot ID:
P0AFI0
Molecular weight:
60581
Reactions
Oxalyl-CoA = formyl-CoA + CO(2).
Protein Details
2. Formyl-coenzyme A transferase
General function:
Involved in catalytic activity
Specific function:
Catalyzes the transfer of the CoA moiety from formyl-CoA to oxalate
Gene Name:
frc
Uniprot ID:
P69902
Molecular weight:
45828
Reactions
Formyl-CoA + oxalate = formate + oxalyl-CoA.