Heme (YMDB00041)

Identification
YMDB IDYMDB00041
NameHeme
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionProtoheme IX (heme b or heme) is the final product in the heme biosynthesis from uroporphyrinogen-III pathway. It is an iron-containing prosthetic group found in many essential proteins including cytochromes and heme-containing globins. In addition to its role in oxidative metabolism, heme also functions as a regulatory molecule in transcription, translation, protein targeting, protein stability, and cellular differentiation. 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 PWY-5189]
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • (protoporphyrinato)iron
  • Ferroheme
  • Ferroheme b
  • Ferroprotoheme
  • Ferroprotoporphyrin
  • Ferroprotoporphyrin IX
  • Ferrous protoheme
  • Ferrous protoheme IX
  • Haem
  • Hem
  • Heme
  • Iron protoporphyrin
  • Iron protoporphyrin IX
  • Iron(II) protoporphyrin IX
  • Protoferroheme
  • Protohaem
  • Protoheme
  • Protoheme IX
  • Reduced hematin
CAS number14875-96-8
WeightAverage: 616.487
Monoisotopic: 616.177297665
InChI KeyRJNYXPJELPLPLJ-UHFFFAOYSA-N
InChIInChI=1S/C34H32N4O4.Fe/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;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H,39,40)(H,41,42);/q-2;+4
IUPAC NameNot Available
Traditional IUPAC NameNot Available
Chemical FormulaC34H32FeN4O4
SMILES[H]OC(=O)C([H])([H])C([H])([H])C1=C(C2=C([H])C3=[N]4C(=C([H])C5=[N]6C(=C([H])C7=C(C(=C8C([H])=C1N2[Fe++]46N78)C([H])([H])C([H])([H])C(=O)O[H])C([H])([H])[H])C(C([H])=C([H])[H])=C5C([H])([H])[H])C(C([H])=C([H])[H])=C3C([H])([H])[H])C([H])([H])[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as metallotetrapyrroles. These are polycyclic compounds containing a tetrapyrrole skeleton combined with a metal atom.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassTetrapyrroles and derivatives
Sub ClassMetallotetrapyrroles
Direct ParentMetallotetrapyrroles
Alternative Parents
Substituents
  • Metallotetrapyrrole skeleton
  • Dicarboxylic acid or derivatives
  • Substituted pyrrole
  • Pyrrole
  • Heteroaromatic compound
  • Carboxylic acid derivative
  • Carboxylic acid
  • Metalloheterocycle
  • Organic transition metal salt
  • Organic metal salt
  • Azacycle
  • Organic oxide
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Organic salt
  • Carbonyl group
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic cation
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateSolid
Charge2
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.0012 g/LALOGPS
logP2ALOGPS
logS-5.8ALOGPS
Physiological Charge2ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area121.19 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity176.19 m³·mol⁻¹ChemAxon
Polarizability69.92 ųChemAxon
Number of Rings8ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • mitochondrion
Organoleptic PropertiesNot Available
SMPDB Pathways
Oxidative phosphorylationPW002461 ThumbThumb?image type=greyscaleThumb?image type=simple
Porphyrin MetabolismPW002462 ThumbThumb?image type=greyscaleThumb?image type=simple
Steroid biosynthesisPW002482 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Oxidative phosphorylationec00190 Map00190
Porphyrin and chlorophyll metabolismec00860 Map00860
Steroid biosynthesisec00100 Map00100
SMPDB Reactions
Protoporphyrin IX + Iron(2+) → Heme + Hydrogen
Heme + Farnesyl pyrophosphate → Heme O
Heme + AH2 + oxygen → Biliverdin + Iron(2+) + Carbon monoxide + A + water
KEGG Reactions
Iron(2+) + Protoporphyrin IX → Heme + hydron
water + Heme + 2-trans,6-trans-farnesyl diphosphate → Pyrophosphate + heme o
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
SpectraNot Available
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
  • Enosawa, S., Ohashi, A. (1986). "Localization of enzyme for heme attachment to apocytochrome c in yeast mitochondria." Biochem Biophys Res Commun 141:1145-1150.3028387
  • 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 ID17627
HMDB IDHMDB03178
Pubchem Compound ID26945
Kegg IDC00032
ChemSpider ID7289
FOODB IDNot Available
WikipediaHeme_b
BioCyc IDPROTOHEME

Enzymes

Protein Details
1. Cytochrome c heme lyase
General function:
Involved in holocytochrome-c synthase activity
Specific function:
Links covalently the heme group to the apoprotein of cytochrome c
Gene Name:
CYC3
Uniprot ID:
P06182
Molecular weight:
30080.69922
Reactions
Holocytochrome c → apocytochrome c + heme.
Protein Details
2. 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+).