Precorrin 2 (ECMDB20183) (M2MDB001029)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (886)
Record Information
Version2.0
Creation Date2012-05-31 14:31:55 -0600
Update Date2015-06-03 17:19:28 -0600
Secondary Accession Numbers
  • ECMDB20183
Identification
Name:Precorrin 2
DescriptionPrecorrin 2 is a member of the chemical class 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. Precorrin 2 is invovled in Proto- and siroheme biosynthesis. Precorrin-2 is a precursor of both siroheme and B12. (PMID 8955319)
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 15,23-Dihydrosirohydrochlorin
  • Dihydrosirohydrochlorin
  • Precorrin-2
Chemical Formula:C42H46N4O16
Weight:Average: 862.8318
Monoisotopic: 862.290881444
InChI Key:KVFNZYKFDBWLHT-ZTKUHGNGSA-N
InChI:InChI=1S/C42H46N4O16/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/h14-16,23-24H,3-13,17-18H2,1-2H3,(H9,43,44,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62)/t23-,24-,41+,42+/m1/s1
CAS number:82542-92-5
IUPAC Name:(4S,5S,9S,10S)-4,9,15,19-tetrakis(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(24),7,11(23),12,14,16(22),18-nonaen-22-ium-21-ide
Traditional IUPAC Name:(4S,5S,9S,10S)-4,9,15,19-tetrakis(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(24),7,11(23),12,14,16(22),18-nonaen-22-ium-21-ide
SMILES:[H][C@@]1(CCC(O)=O)C2=CC3=C(CC(O)=O)C(CCC(O)=O)=C(CC4=[NH+]C(=CC5=NC(=CC(=N2)[C@@]1(C)CC(O)=O)[C@@]([H])(CCC(O)=O)[C@]5(C)CC(O)=O)C(CC(O)=O)=C4CCC(O)=O)[N-]3
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
  • Heteroaromatic compound
  • Pyrroline
  • Pyrrole
  • Ketimine
  • Azacycle
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic zwitterion
  • Organooxygen compound
  • Organonitrogen compound
  • Imine
  • Carbonyl group
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
State:Not Available
Charge:-8
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.026 g/LALOGPS
logP1.04ALOGPS
logP1.57ChemAxon
logS-4.5ALOGPS
pKa (Strongest Acidic)3.15ChemAxon
Physiological Charge-8ChemAxon
Hydrogen Acceptor Count19ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area349.98 ŲChemAxon
Rotatable Bond Count20ChemAxon
Refractivity227.83 m³·mol⁻¹ChemAxon
Polarizability86.93 ųChemAxon
Number of Rings5ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
2 S-Adenosylmethionine + Uroporphyrinogen III >2 S-Adenosylhomocysteine + Precorrin 2 + Hydrogen ion
Precorrin 2 + NAD > Hydrogen ion + NADH + Sirohydrochlorin
2 S-Adenosylmethionine + Uroporphyrinogen III <>2 S-Adenosylhomocysteine + Precorrin 2
Precorrin 2 + NAD <> Sirohydrochlorin + NADH + Hydrogen ion
S-Adenosylmethionine + precorrin-1 > S-Adenosylhomocysteine + Precorrin 2
2 S-Adenosylmethionine + Uroporphyrinogen III + Precorrin-1 <>2 S-Adenosylhomocysteine + Precorrin 2
Precorrin 2 + NAD <> Sirohydrochlorin + NADH +2 Hydrogen ion
2 S-Adenosylmethionine + Uroporphyrinogen III >2 S-Adenosylhomocysteine + Precorrin 2 + Hydrogen ion
2 S-Adenosylmethionine + Uroporphyrinogen III >2 S-Adenosylhomocysteine + Precorrin 2 + Hydrogen ion
SMPDB Pathways:
Porphyrin metabolismPW000936 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-01t9-0000000090-3fed12fcc4f9b8f249e6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-0000000090-457d3e08ad7483db3c02View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0bt9-0120001090-deb3d0f24e6ef8da71baView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-0000000090-bcea32de04cd450f7babView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03fr-1000000090-b4be0b8b43691ca31dcfView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-7000001090-52f742092fbf18c1b905View in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Fazzio, T. G., Roth, J. R. (1996). "Evidence that the CysG protein catalyzes the first reaction specific to B12 synthesis in Salmonella typhimurium, insertion of cobalt." J Bacteriol 178:6952-6959. Pubmed: 8955319
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID50602
HMDB IDNot Available
Pubchem Compound ID5280516
Kegg IDC02463
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDDIHYDROSIROHYDROCHLORIN
EcoCyc IDDIHYDROSIROHYDROCHLORIN

Enzymes

Protein Details
1. Putative uroporphyrinogen-III C-methyltransferase
General function:
Coenzyme transport and metabolism
Specific function:
S-adenosyl-L-methionine + uroporphyrinogen III = S-adenosyl-L-homocysteine + precorrin-1
Gene Name:
hemX
Uniprot ID:
P09127
Molecular weight:
42963
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 synthase
General function:
Involved in methyltransferase activity
Specific function:
Multifunctional enzyme that catalyzes the SAM-dependent methylation of uroporphyrinogen III at position C-2 and C-7 to form precorrin-2 and then position C-12 or C-18 to form trimethylpyrrocorphin 2. It also catalyzes the conversion of precorrin-2 into siroheme. This reaction consists of the NAD- dependent oxidation of precorrin-2 into sirohydrochlorin and its subsequent ferrochelation into siroheme
Gene Name:
cysG
Uniprot ID:
P0AEA8
Molecular weight:
49951
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.
Precorrin-2 + NAD(+) = sirohydrochlorin + NADH.
Siroheme + 2 H(+) = sirohydrochlorin + Fe(2+).