Protoporphyrin IX (YMDB00055)

Identification
YMDB IDYMDB00055
NameProtoporphyrin IX
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionProtoporphyrin IX is an intermediate in the heme biosynthesis from uroporphyrinogen-III pathway. In this pathway, protoporphyrin IX is obtained from protoporphyrinogen IX and converted to protoheme 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
  • 3,3'-(3,7,12,17-tetramethyl-8,13-divinyl-21H,23H-porphine-2,18-diyl)-bis-propionate
  • 3,3'-(3,7,12,17-tetramethyl-8,13-divinyl-21H,23H-porphine-2,18-diyl)-bis-propionic acid
  • 3,3'-(3,7,12,17-tetramethyl-8,13-divinylporphine-2,18-diyl)di
  • 3,7,12,17-Tetramethyl-8,13-divinylporphyrin-2,18-dipropanoate
  • 3,7,12,17-Tetramethyl-8,13-divinylporphyrin-2,18-dipropanoic acid
  • H2PpIX
  • Kammerer's prophyrin
  • Ooporphyrin
  • Porphyrinogen IX
  • ppIX
  • Protoporphyrin
  • Protoporphyrin IX
  • Protoporphyrin-"ix"
  • protoporphyrin-IX
CAS number553-12-8
WeightAverage: 562.6582
Monoisotopic: 562.258005596
InChI KeyKSFOVUSSGSKXFI-UJJXFSCMSA-N
InChIInChI=1S/C34H34N4O4/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/h7-8,13-16,35,38H,1-2,9-12H2,3-6H3,(H,39,40)(H,41,42)/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-
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(21),2,4,6,8(23),9,11,13,15,17,19-undecaen-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(21),2,4,6,8(23),9,11,13,15,17,19-undecaen-4-yl]propanoic acid
Chemical FormulaC34H34N4O4
SMILES[H]OC(=O)C([H])([H])C([H])([H])C1=C(\C2=C([H])\C3=C(C(C([H])=C([H])[H])=C(N3[H])\C([H])=C3/N=C(/C(/[H])=C4\N([H])\C(=C([H])/C1=N2)C(=C4C([H])([H])[H])C([H])([H])C([H])([H])C(=O)O[H])C(C([H])=C([H])[H])=C3C([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 ParentsNot Available
SubstituentsNot Available
Molecular FrameworkNot Available
External DescriptorsNot Available
Physical Properties
StateSolid
Charge0
Melting point300 °C
Experimental Properties
PropertyValueReference
Water Solubility0.169 mg/mL at 25 oC [YALKOWSKY,SH & DANNENFELSER,RM (1992)]PhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.022 g/LALOGPS
logP4.4ALOGPS
logP6.78ChemAxon
logS-4.4ALOGPS
pKa (Strongest Acidic)3.68ChemAxon
pKa (Strongest Basic)4.96ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area131.96 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity163.81 m³·mol⁻¹ChemAxon
Polarizability66.03 ųChemAxon
Number of Rings5ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • mitochondrion
Organoleptic PropertiesNot Available
SMPDB Pathways
Porphyrin MetabolismPW002462 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Porphyrin and chlorophyll metabolismec00860 Map00860
SMPDB Reactions
Protoporphyrinogen IX + oxygen → Protoporphyrin IX + Hydrogen peroxide
Protoporphyrin IX + Iron(2+) → Heme + Hydrogen
KEGG Reactions
Iron(2+) + Protoporphyrin IX → Heme + hydron
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, Positivesplash10-0uxu-1000290000-e22236fe3cca8eed1ecfJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00di-6000094000-b9c12952e100c5144cabJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS ("Protoporphyrin IX,1TMS,#1" TMS) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_1) - 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_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 (TBDMS_1_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_4) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_5) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_6) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0002-0000090000-5d5be53410134c5719abJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00kb-1000590000-2d4157b9f73534d95a9cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4l-1000910000-07524a9291a1921dfafcJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-0000090000-5df26c1cfb9a0b16a91aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0296-1000190000-2d4bcb49201fc10adc09JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4l-9000230000-064fb944a966d08c06bfJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-0000090000-87c1740ecd1a28f4a2d9JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03xu-0000590000-99160b987bb7e62ab362JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00di-0000900000-f2d9118441a9c8c47d79JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03dj-0000090000-d428ac6dc2fc4794cc41JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0j4j-0000090000-2b065966ec57bb97d511JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0uk9-1000970000-b435817e4dc349e65ab3JSpectraViewer
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
  • Strakhovskaia, M. G., Shumarina, A. O., Fraikin, G. I. a., Rubin, A. B. (2002). "[Fluorescent photobleaching of endogenous protoporphyrin IX in yeast cells]." Biofizika 47:852-857.12397956
  • Strakhovskaya, M. G., Shumarina, A. O., Fraikin, G. Y. a., Rubin, A. B. (1999). "Endogenous porphyrin accumulation and photosensitization in the yeast Saccharomyces cerevisiae in the presence of 2,2'-dipyridyl." J Photochem Photobiol B 49:18-22.10365443
  • 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:Games, David E.; Jackson, Anthony H.; Jackson, J. Richard; Belcher, Roderick V.; Smith, Sydney G. Biosynthesis of protoporphyrin-IX from coproporphyrinogen-III. Journal of the Chemical Society, Chemical Communications (1976), (6), 187-8.
External Links:
ResourceLink
CHEBI ID15430
HMDB IDHMDB00241
Pubchem Compound ID4971
Kegg IDC02191
ChemSpider ID10469486
FOODB IDFDB004277
WikipediaProtoporphyrin_IX
BioCyc IDPROTOPORPHYRIN_IX

Enzymes

Protein Details
1. Ferrochelatase, mitochondrial
General function:
Involved in ferrochelatase activity
Specific function:
Catalyzes the ferrous insertion into protoporphyrin IX
Gene Name:
HEM15
Uniprot ID:
P16622
Molecular weight:
44595.80078
Reactions
Protoheme + 2 H(+) → protoporphyrin + Fe(2+).
Protein Details
2. 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).