Sirohydrochlorin (YMDB00249)

Identification
YMDB IDYMDB00249
NameSirohydrochlorin
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionSirohydrochlorin is an intermediate in the last step of 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
  • (7S,8S,12S,13S)-3,8,13,17-tetrakis(carboxymethyl)-8,13-dimethyl-7,8,12,13-tetrahydroporphyrin-2,7,12,18-tetrapropionic acid
  • Dihydrosirohydrochlorin
  • Precorrin 2
  • Sirohydrochlorin
  • (7S,8S,12S,13S)-3,8,13,17-Tetrakis(carboxymethyl)-8,13-dimethyl-7,8,12,13-tetrahydroporphyrin-2,7,12,18-tetrapropionate
CAS number65207-12-7
WeightAverage: 862.8318
Monoisotopic: 862.290881444
InChI KeyKWIZRXMMFRBUML-AHGFGAHVSA-N
InChIInChI=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/h13-16,23-24,44-45H,3-12,17-18H2,1-2H3,(H,47,48)(H,49,50)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H,59,60)(H,61,62)/b25-13-,29-14-,31-15-,32-16-/t23-,24-,41+,42+/m1/s1
IUPAC Name3-[(4S,5S,9S,10S)-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(21),2,6,8(23),11,13,15,17,19-nonaen-4-yl]propanoic acid
Traditional IUPAC Namesirohydrochlorin
Chemical FormulaC42H46N4O16
SMILESC[C@]1(CC(O)=O)[C@H](CCC(O)=O)\C2=C\C3=N\C(=C/C4=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)\C(CCC(O)=O)=C3CC(O)=O
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
  • Heteroaromatic compound
  • Carboxylic acid derivative
  • Carboxylic acid
  • Azacycle
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • 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 Solubility0.025 g/LALOGPS
logP1.04ALOGPS
logP3.12ChemAxon
logS-4.5ALOGPS
pKa (Strongest Acidic)3.06ChemAxon
Physiological Charge-8ChemAxon
Hydrogen Acceptor Count18ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area355.76 ŲChemAxon
Rotatable Bond Count20ChemAxon
Refractivity209.38 m³·mol⁻¹ChemAxon
Polarizability89.44 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
Sirohydrochlorin + Iron(2+) → hydron + Siroheme
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-002b-0000000590-ed03bd2dfabb11dffa05JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-006t-0000000940-5b3a240ffe55a81be5b8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0avi-0000000920-e98aa012967f148e1d86JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0301-0000000790-d2080d5c77f3c757c10eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00r2-0000000950-fad195608adfddb030b6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-052b-2000000930-856c98525e7bd6b9a47cJSpectraViewer
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
  • 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 ID18023
HMDB IDNot Available
Pubchem Compound ID196427
Kegg IDC02463
ChemSpider ID24808091
FOODB IDNot Available
Wikipedia IDSirohydrochlorin
BioCyc IDNot Available

Enzymes

Protein Details
1. 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+).