Protoporphyrinogen IX (YMDB00156)

Identification
YMDB IDYMDB00156
NameProtoporphyrinogen IX
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionProtoporphyrinogen IX is an intermediate in the heme biosynthesis from uroporphyrinogen-III pathway. In this pathway, protoporphyrinogen IX is obtained from coproporphyrinogen III and converted to protoporphyrin IX. Protoheme IX is the final product in this pathway but different derivatives of protoheme can actually be formed that differ in modifications to the porphyrin ring, including how it is bound to the protein (e.g. heme o, heme a, heme c, and heme d). [Biocyc HEME-BIOSYNTHESIS-II]
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 7,12-diethenyl-3,8,13,17-tetramethyl-5,10,15,20,22,24-hexahydroporphyrin-2,18-dipropanoate
  • 7,12-diethenyl-3,8,13,17-tetramethyl-5,10,15,20,22,24-hexahydroporphyrin-2,18-dipropanoic acid
  • 7,12-diethenyl-5,10,15,20,22,24-hexahydro-3,8,13,17-tetramethyl-21h,23h-porphine-2,18-dipropanoate
  • 7,12-diethenyl-5,10,15,20,22,24-hexahydro-3,8,13,17-tetramethyl-21h,23h-porphine-2,18-dipropanoic acid
  • Protoporphyrinogen
  • protoporphyrinogen IX
  • protoporphyrinogen-IX
  • 5,10,15,20,22,24-Hexahydro protoporphyrin IX deriv.
CAS number7412-77-3
WeightAverage: 568.7058
Monoisotopic: 568.304955788
InChI KeyUHSGPDMIQQYNAX-UHFFFAOYSA-N
InChIInChI=1S/C34H40N4O4/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25/h7-8,35-38H,1-2,9-16H2,3-6H3,(H,39,40)(H,41,42)
IUPAC Name3-[20-(2-carboxyethyl)-9,14-diethenyl-5,10,15,19-tetramethyl-21,22,23,24-tetraazapentacyclo[16.2.1.1^{3,6}.1^{8,11}.1^{13,16}]tetracosa-1(20),3,5,8,10,13,15,18-octaen-4-yl]propanoic acid
Traditional IUPAC Name3-[20-(2-carboxyethyl)-9,14-diethenyl-5,10,15,19-tetramethyl-21,22,23,24-tetraazapentacyclo[16.2.1.1^{3,6}.1^{8,11}.1^{13,16}]tetracosa-1(20),3,5,8,10,13,15,18-octaen-4-yl]propanoic acid
Chemical FormulaC34H40N4O4
SMILES[H]OC(=O)C([H])([H])C([H])([H])C1=C2N([H])C(=C1C([H])([H])[H])C([H])([H])C1=C(C([H])=C([H])[H])C(=C(N1[H])C([H])([H])C1=C(C([H])=C([H])[H])C(=C(N1[H])C([H])([H])C1=C(C(=C(N1[H])C2([H])[H])C([H])([H])C([H])([H])C(=O)O[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[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
  • Dicarboxylic acid or derivatives
  • Substituted pyrrole
  • Pyrrole
  • Heteroaromatic compound
  • Azacycle
  • Carboxylic acid
  • Carboxylic acid derivative
  • Carbonyl group
  • Organopnictogen compound
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • 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 Solubility0.0055 g/LALOGPS
logP3.44ALOGPS
logP6.2ChemAxon
logS-5ALOGPS
pKa (Strongest Acidic)4.07ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area137.76 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity169.42 m³·mol⁻¹ChemAxon
Polarizability64.52 ųChemAxon
Number of Rings5ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • mitochondrion
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Porphyrin MetabolismPW002462 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Porphyrin and chlorophyll metabolismec00860 Map00860
SMPDB Reactions
Coproporphyrinogen III + oxygen + Hydrogen → Protoporphyrinogen IX + Carbon dioxide + water
Protoporphyrinogen IX + oxygen → Protoporphyrin IX + Hydrogen peroxide
KEGG Reactions
Coproporphyrinogen III + oxygen + hydron → water + Carbon dioxide + Protoporphyrinogen IX
oxygen + Protoporphyrinogen IX → water + Protoporphyrin IX
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0pi3-1000190000-2785151d048ffcfdafc1JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00bc-9000053000-45009d4bbcc7a57d2e8bJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS ("Protoporphyrinogen IX,1TMS,#1" TMS) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_12) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_13) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_14) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_15) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0000190000-7c4ce83e3be73bfccdf6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0pi0-0000490000-affa2d20d85ce7a5a2a1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03dj-0020900000-a1714c4d96457c66da57JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-0000090000-4148fa37b5b91e3b5a92JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-05tb-1000090000-27a9f5ba745bc29e2b22JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-9000260000-392765703d0911aa98fcJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0gb9-0000090000-9a1be7ce809937d54938JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0ldi-0000190000-1a53eff6b6eaea2bd1a8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-0000790000-030a68500ee48fd68e34JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014j-0000090000-4f79e644c71d1a64565bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-014j-0000090000-8599f24133cbc58316ebJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-1000950000-a5525829d1d51b8650b0JSpectraViewer
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 ID15435
HMDB IDHMDB01097
Pubchem Compound ID121893
Kegg IDC01079
ChemSpider ID108741
FOODB IDFDB022425
WikipediaProtoporphyrinogen_IX
BioCyc IDPROTOPORPHYRINOGEN

Enzymes

Protein Details
1. Protoporphyrinogen oxidase
General function:
Involved in oxygen-dependent protoporphyrinogen oxidase activity
Specific function:
Catalyzes the 6-electron oxidation of protoporphyrinogen-IX to form protoporphyrin-IX
Gene Name:
HEM14
Uniprot ID:
P40012
Molecular weight:
59702.39844
Reactions
Protoporphyrinogen-IX + 3 O(2) → protoporphyrin-IX + 3 H(2)O(2).
Protein Details
2. Coproporphyrinogen-III oxidase
General function:
Involved in coproporphyrinogen oxidase activity
Specific function:
Key enzyme in heme biosynthesis. Catalyzes the oxidative decarboxylation of propionic acid side chains of rings A and B of coproporphyrinogen III
Gene Name:
HEM13
Uniprot ID:
P11353
Molecular weight:
37711.30078
Reactions
Coproporphyrinogen-III + O(2) + 2 H(+) → protoporphyrinogen-IX + 2 CO(2) + 2 H(2)O.