Precorrin-2 (YMDB00977)

Identification
YMDB IDYMDB00977
NamePrecorrin-2
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionPrecorrin-2 is an intermediate in the siroheme biosynthesis pathway. Siroheme is an iron-containing isobacteriochlorin, a modified tetrapyrrole similar in structure to both heme and chlorophyll. Siroheme is found as a prosthetic group of several enzymes, including sulfite and nitrite reductases, which catalyze the six-electron reductions of sulfite to sulfide and nitrite to ammonia, respectively. Siroheme biosynthesis starts by the same route as other tetrapyrroles, the synthesis of the intermediate uroporphyrinogen-III. [Biocyc PWY-5194]
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 15,23-Dihydrosirohydrochlorin
  • Dihydrosirohydrochlorin
  • Precorrin 2
CAS number82542-92-5
WeightAverage: 864.8477
Monoisotopic: 864.306531508
InChI KeyOQIIYZQTTMKFAU-ZNLOQLQNSA-N
InChIInChI=1S/C42H48N4O16/c1-41(17-39(59)60)23(5-9-35(51)52)29-14-27-21(11-37(55)56)19(3-7-33(47)48)25(43-27)13-26-20(4-8-34(49)50)22(12-38(57)58)28(44-26)15-31-42(2,18-40(61)62)24(6-10-36(53)54)30(46-31)16-32(41)45-29/h14-16,23-24,43-45H,3-13,17-18H2,1-2H3,(H,47,48)(H,49,50)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H,59,60)(H,61,62)/b29-14-,31-15-,32-16-/t23-,24-,41+,42+/m1/s1
IUPAC Name3-[(4S,5S,6Z,9S,10S,11Z)-9,15,19-tris(2-carboxyethyl)-5,10,14,20-tetrakis(carboxymethyl)-5,10-dimethyl-21,22,23,24-tetraazapentacyclo[16.2.1.1³,⁶.1⁸,¹¹.1¹³,¹⁶]tetracosa-1(20),2,6,8(23),11,13,15,18-octaen-4-yl]propanoic acid
Traditional IUPAC Name3-[(4S,5S,6Z,9S,10S,11Z)-9,15,19-tris(2-carboxyethyl)-5,10,14,20-tetrakis(carboxymethyl)-5,10-dimethyl-21,22,23,24-tetraazapentacyclo[16.2.1.1³,⁶.1⁸,¹¹.1¹³,¹⁶]tetracosa-1(20),2,6,8(23),11,13,15,18-octaen-4-yl]propanoic acid
Chemical FormulaC42H48N4O16
SMILESC[C@]1(CC(O)=O)[C@H](CCC(O)=O)\C2=C\C3=C(CC(O)=O)C(CCC(O)=O)=C(CC4=C(CCC(O)=O)C(CC(O)=O)=C(N4)\C=C4/N=C(/C=C1\N2)[C@@H](CCC(O)=O)[C@]4(C)CC(O)=O)N3
Chemical Taxonomy
Description belongs to the class of organic compounds known as tetrapyrroles and derivatives. These are polycyclic aromatic compounds containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassTetrapyrroles and derivatives
Sub ClassNot Available
Direct ParentTetrapyrroles and derivatives
Alternative Parents
Substituents
  • Tetrapyrrole skeleton
  • Substituted pyrrole
  • Pyrrole
  • Pyrrolidine
  • Pyrroline
  • Heteroaromatic compound
  • Amino acid
  • Amino acid or derivatives
  • Ketimine
  • Azacycle
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carboxylic acid derivative
  • Carboxylic acid
  • Secondary amine
  • Secondary aliphatic amine
  • Enamine
  • Organopnictogen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Imine
  • Amine
  • Organic nitrogen compound
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic oxide
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateNot Available
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.034 g/LALOGPS
logP1.07ALOGPS
logP1.09ChemAxon
logS-4.4ALOGPS
pKa (Strongest Acidic)2.91ChemAxon
Physiological Charge-7ChemAxon
Hydrogen Acceptor Count18ChemAxon
Hydrogen Donor Count11ChemAxon
Polar Surface Area354.37 ŲChemAxon
Rotatable Bond Count20ChemAxon
Refractivity217.23 m³·mol⁻¹ChemAxon
Polarizability89.13 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 PathwaysNot Available
KEGG Pathways
Porphyrin and chlorophyll metabolismec00860 Map00860
SMPDB ReactionsNot Available
KEGG Reactions
NADP + Precorrin-2 → Sirohydrochlorin + NADPH + hydron
Uroporphyrinogen III + S-Adenosylmethionine → Precorrin-2 + S-Adenosylhomocysteine + hydron
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0fb9-0000000190-9b167b59d9abd2a783c1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0000000490-7bd7c85fd12c743a7db9JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0ug0-0000000960-4452e95e69c535fab480JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0i29-0000000390-07b38a93562a1fe0072fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0v00-0000000590-8c758644ab7e6fbd0d7aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0zfr-2000000490-71f620321f14146ad7c4JSpectraViewer
MSMass Spectrum (Electron Ionization)Not 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
  • Raux, E., McVeigh, T., Peters, S. E., Leustek, T., Warren, M. J. (1999). "The role of Saccharomyces cerevisiae Met1p and Met8p in sirohaem and cobalamin biosynthesis." Biochem J 338 ( Pt 3):701-708.10051442
  • Schubert, H. L., Raux, E., Brindley, A. A., Leech, H. K., Wilson, K. S., Hill, C. P., Warren, M. J. (2002). "The structure of Saccharomyces cerevisiae Met8p, a bifunctional dehydrogenase and ferrochelatase." EMBO J 21:2068-2075.11980703
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID50602
HMDB IDNot Available
Pubchem Compound ID25245987
Kegg IDC02463
ChemSpider ID24808156
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

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. Siroheme biosynthesis protein MET8
General function:
Involved in binding
Specific function:
Catalyzes the conversion of precorrin-2 into siroheme. This reaction consist of the NAD-dependent oxidation of precorrin- 2 into sirohydrochlorin and its subsequent ferrochelation into siroheme
Gene Name:
MET8
Uniprot ID:
P15807
Molecular weight:
31917.40039
Reactions
Precorrin-2 + NAD(+) → sirohydrochlorin + NADH.
Siroheme + 2 H(+) → sirohydrochlorin + Fe(2+).