You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.

Uroporphyrinogen III (YMDB00267)

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
MOLSDFPDBSMILESInChI
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
Hydroxymethylbilane → Uroporphyrinogen III + water
Uroporphyrinogen III → Coproporphyrinogen III + Carbon dioxide
KEGG Reactions
Uroporphyrinogen III + hydron → Coproporphyrinogen III + Carbon dioxide
Uroporphyrinogen III + S-Adenosylmethionine → Precorrin-2 + S-Adenosylhomocysteine + hydron
Hydroxymethylbilane → Uroporphyrinogen 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
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00xr-0000000950-9b8035c556d329d65d92JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-008a-0000000900-ca31eaf24646ca5e9004JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0032-0000000900-42e2c47ece780e68ce9cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00dj-0000000900-efbf6751227445074375JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0002-0000000900-1faa99e113ce7b175d67JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00kb-0000000900-479f518906c52f496e89JSpectraViewer
MSMass Spectrum (Electron Ionization)Not AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
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 IDFDB022417
WikipediaUroporphyrinogen_III
BioCyc IDUROPORPHYRINOGEN-III

Enzymes

Protein Details
1. Uroporphyrinogen-III C-methyltransferase
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.
Protein Details
2. Uroporphyrinogen decarboxylase
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).
Protein Details
3. Uroporphyrinogen-III synthase
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.