You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.
Identification
YMDB IDYMDB00267
NameUroporphyrinogen III
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionUroporphyrinogen-III is the final product in tetrapyrrole biosynthesis pathway which starts with the formation of 5-aminolevulinic acid from glycine and succinyl CoA by the enzyme ALA synthase. Uroporphyrinogen-III is a major branch point that leads to biosynthesis of different tetrapyrrole compounds (e.g. porphyrins). Tetrapyrroles usually function as a metal-binding cofactor in many important enzymes, proteins and pigments, such as heme, chlorophyll, cobalamine, siroheme, and cofator F430. [Biocyc PWY-5189]
Structure
Thumb
Synonyms
  • 3,8,13,17-tetrakis(carboxymethyl)-5,10,15,20,22,24-hexahydro-2,7,12,18-Porphinetetrapropionate
  • 3,8,13,17-tetrakis(carboxymethyl)-5,10,15,20,22,24-hexahydro-2,7,12,18-Porphinetetrapropionic acid
  • 3,8,13,17-tetrakis(carboxymethyl)-5,10,15,20,22,24-hexahydro-21H,23H-Porphine-2,7,12,18-tetrapropanoate
  • 3,8,13,17-tetrakis(carboxymethyl)-5,10,15,20,22,24-hexahydro-21H,23H-Porphine-2,7,12,18-tetrapropanoic acid
  • 3,8,13,17-tetrakis(carboxymethyl)-5,10,15,20,22,24-hexahydroporphyrin-2,7,12,18-tetrapropanoate
  • 3,8,13,17-tetrakis(carboxymethyl)-5,10,15,20,22,24-hexahydroporphyrin-2,7,12,18-tetrapropanoic acid
  • Urogen III
  • Uroporphyrinogen III
  • uroporphyrinogen-III
  • 3,8,13,17-Tetrakis(carboxymethyl)-5,10,15,20,22,24-hexahydroporphyrin-2,7,12,18-tetrapropionic acid
  • Uro'gen III
  • 3,8,13,17-Tetrakis(carboxymethyl)-5,10,15,20,22,24-hexahydroporphyrin-2,7,12,18-tetrapropionate
  • Uroporphyrinogens
CAS number1976-85-8
WeightAverage: 836.7946
Monoisotopic: 836.27523138
InChI KeyHUHWZXWWOFSFKF-UHFFFAOYSA-N
InChIInChI=1S/C40H44N4O16/c45-33(46)5-1-17-21(9-37(53)54)29-14-27-19(3-7-35(49)50)22(10-38(55)56)30(43-27)15-28-20(4-8-36(51)52)24(12-40(59)60)32(44-28)16-31-23(11-39(57)58)18(2-6-34(47)48)26(42-31)13-25(17)41-29/h41-44H,1-16H2,(H,45,46)(H,47,48)(H,49,50)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H,59,60)
IUPAC Name3-[9,14,20-tris(2-carboxyethyl)-5,10,15,19-tetrakis(carboxymethyl)-21,22,23,24-tetraazapentacyclo[16.2.1.1³,⁶.1⁸,¹¹.1¹³,¹⁶]tetracosa-1(20),3,5,8,10,13,15,18-octaen-4-yl]propanoic acid
Traditional IUPAC Nameuroporphyrinogen-III
Chemical FormulaC40H44N4O16
SMILES[H]OC(=O)C([H])([H])C1=C2N([H])C(=C1C([H])([H])C([H])([H])C(=O)O[H])C([H])([H])C1=C(C(=C(N1[H])C([H])([H])C1=C(C(=C(N1[H])C([H])([H])C1=C(C(=C(N1[H])C2([H])[H])C([H])([H])C(=O)O[H])C([H])([H])C([H])([H])C(=O)O[H])C([H])([H])C([H])([H])C(=O)O[H])C([H])([H])C(=O)O[H])C([H])([H])C([H])([H])C(=O)O[H])C([H])([H])C(=O)O[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as porphyrins. Porphyrins are compounds containing a fundamental skeleton of four pyrrole nuclei united through the alpha-positions by four methine groups to form a macrocyclic structure.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassTetrapyrroles and derivatives
Sub ClassPorphyrins
Direct ParentPorphyrins
Alternative Parents
Substituents
  • Porphyrin
  • Substituted pyrrole
  • Pyrrole
  • Heteroaromatic compound
  • Carboxylic acid derivative
  • Carboxylic acid
  • Azacycle
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.044 g/LALOGPS
logP0.67ALOGPS
logP1.39ChemAxon
logS-4.3ALOGPS
pKa (Strongest Acidic)3.21ChemAxon
Physiological Charge-8ChemAxon
Hydrogen Acceptor Count16ChemAxon
Hydrogen Donor Count12ChemAxon
Polar Surface Area361.56 ŲChemAxon
Rotatable Bond Count20ChemAxon
Refractivity206.93 m³·mol⁻¹ChemAxon
Polarizability81.55 ųChemAxon
Number of Rings5ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Porphyrin MetabolismPW002462 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Porphyrin and chlorophyll metabolismec00860 Map00860
SMPDB Reactions
HydroxymethylbilaneUroporphyrinogen III + water
Uroporphyrinogen IIICoproporphyrinogen III + Carbon dioxide
KEGG Reactions
Uroporphyrinogen III + hydronCoproporphyrinogen III + Carbon dioxide
Uroporphyrinogen III + S-AdenosylmethioninePrecorrin-2 + S-Adenosylhomocysteine + hydron
HydroxymethylbilaneUroporphyrinogen III + water
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-106r-0000000980-8aa242b9a95e3ad92890JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-05fr-0000000910-5ea901953b2295eabfb6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0ab9-0000000900-fe3587925504317b1a70JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00xr-0000000930-6a464d08b50b7b5e266cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00di-0000000910-22d2fcd94b453076587dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00di-2000000900-342f06471315f49e3debJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Chelstowska, A., Rytka, J. (1993). "[Biosynthesis of heme in yeast Saccharomyces cerevisiae]." Postepy Biochem 39:173-185.8234090
  • Hoffman, M., Gora, M., Rytka, J. (2003). "Identification of rate-limiting steps in yeast heme biosynthesis." Biochem Biophys Res Commun 310:1247-1253.14559249
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID15437
HMDB IDHMDB01086
Pubchem Compound ID1179
Kegg IDC01051
ChemSpider ID1146
FOODB IDFDB031250
WikipediaUroporphyrinogen_III
BioCyc IDUROPORPHYRINOGEN-III

Enzymes

General function:
Involved in methyltransferase activity
Specific function:
Siroheme synthase involved in methionine biosynthesis
Gene Name:
MET1
Uniprot ID:
P36150
Molecular weight:
66124.70313
Reactions
S-adenosyl-L-methionine + uroporphyrinogen III → S-adenosyl-L-homocysteine + precorrin-1.
S-adenosyl-L-methionine + precorrin-1 → S-adenosyl-L-homocysteine + precorrin-2.
General function:
Involved in uroporphyrinogen decarboxylase activity
Specific function:
Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III
Gene Name:
HEM12
Uniprot ID:
P32347
Molecular weight:
41348.69922
Reactions
Uroporphyrinogen III → coproporphyrinogen + 4 CO(2).
General function:
Involved in uroporphyrinogen-III synthase activity
Specific function:
Catalyzes cyclization of the linear tetrapyrrole, hydroxymethylbilane, to the macrocyclic uroporphyrinogen III
Gene Name:
HEM4
Uniprot ID:
P06174
Molecular weight:
30911.30078
Reactions
Hydroxymethylbilane → uroporphyrinogen III + H(2)O.