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ADP-ribose 1"-2" cyclic phosphate (YMDB00141)

Identification
YMDB IDYMDB00141
NameADP-ribose 1"-2" cyclic phosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionPC(16:1(9Z)/22:0) is a phosphatidylchloline (PC). It is a glycerophospholipid in which a phosphorylcholine moiety occupies a glycerol substitution site. As is the case with diacylglycerols, phosphatidylcholines can have many different combinations of fatty acids of varying lengths and saturation attached to the C-1 and C-2 positions. PC(16:1(9Z)/22:0), in particular, consists of one 9Z-hexadecenoyl chain to the C-1 atom, and one docosanoyl to the C-2 atom. In E. coli, PCs can be found in the integral component of the cell outer membrane. They are hydrolyzed by Phospholipases to a 2-acylglycerophosphocholine and a carboxylate.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • adenosine diphosphate ribose 1"-2" cyclic phosphate
  • ADP ribose 1'',2''-phosphate
  • ADP-ribose 1 ,2 -cyclic phosphate
  • ADP-ribose 1' ,2' -cyclic phosphate
  • {[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}[({[(5R)-2,6-dihydroxy-2-oxo-tetrahydro-2H-2λ⁵-furo[2,3-D][1,3,2]dioxaphosphol-5-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphinate
  • ADP-Ribose 1"-2" cyclic phosphoric acid
CAS numberNot Available
WeightAverage: 621.2804
Monoisotopic: 621.027439217
InChI KeyNPSPRYXPOGPCPM-PNUFQSOHSA-N
InChIInChI=1S/C15H22N5O16P3/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-37(24,25)36-38(26,27)31-2-6-9(22)11-15(33-6)35-39(28,29)34-11/h3-6,8-11,14-15,21-23H,1-2H2,(H,24,25)(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9?,10-,11?,14-,15?/m1/s1
IUPAC Name{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}[({[(5R)-2,6-dihydroxy-2-oxo-tetrahydro-2H-2λ⁵-furo[2,3-d][1,3,2]dioxaphosphol-5-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphinic acid
Traditional IUPAC Name[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy({[(5R)-2,6-dihydroxy-2-oxo-tetrahydro-2λ⁵-furo[2,3-d][1,3,2]dioxaphosphol-5-yl]methoxy(hydroxy)phosphoryl}oxy)phosphinic acid
Chemical FormulaC15H22N5O16P3
SMILES[H]O[C@]1([H])[C@]([H])(O[H])[C@]([H])(O[C@@]1([H])N1C([H])=NC2=C1N=C([H])N=C2N([H])[H])C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])[C@@]1([H])OC2([H])OP(=O)(O[H])OC2([H])C1([H])O[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as phosphatidylcholines. These are glycerophosphocholines in which the two free -OH are attached to one fatty acid each through an ester linkage.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassGlycerophospholipids
Sub ClassGlycerophosphocholines
Direct ParentPhosphatidylcholines
Alternative Parents
Substituents
  • Diacylglycero-3-phosphocholine
  • Phosphocholine
  • Fatty acid ester
  • Dialkyl phosphate
  • Dicarboxylic acid or derivatives
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Fatty acyl
  • Quaternary ammonium salt
  • Tetraalkylammonium salt
  • Carboxylic acid ester
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic nitrogen compound
  • Carbonyl group
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Amine
  • Organic salt
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility4.97 g/LALOGPS
logP-1.3ALOGPS
logP-6.3ChemAxon
logS-2.1ALOGPS
pKa (Strongest Acidic)1.35ChemAxon
pKa (Strongest Basic)5ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area306.82 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity118.22 m³·mol⁻¹ChemAxon
Polarizability49.46 ųChemAxon
Number of Rings5ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular LocationsNot Available
Organoleptic PropertiesNot Available
SMPDB PathwaysNot Available
KEGG PathwaysNot Available
SMPDB ReactionsNot Available
KEGG ReactionsNot Available
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0uec-2692722000-70e78ea7482b32e5f82aJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-0w4m-3661956000-d8ba0f64f367d1c3b65bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0911103000-07a7d4d6ea2a706a4c8bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0910000000-02ee03431ae425e17512JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-2900000000-a79a1a003480f7520fcbJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00e9-0802309000-a9ac1870c3867f3377e3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-1901100000-a8a5ddb63b64b9de8cd8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a7i-3900000000-84b8296b754202fb3e3cJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Steiger, M. A., Jackman, J. E., Phizicky, E. M. (2005). "Analysis of 2'-phosphotransferase (Tpt1p) from Saccharomyces cerevisiae: evidence for a conserved two-step reaction mechanism." RNA 11:99-106.15611300
  • Culver, G. M., McCraith, S. M., Zillmann, M., Kierzek, R., Michaud, N., LaReau, R. D., Turner, D. H., Phizicky, E. M. (1993). "An NAD derivative produced during transfer RNA splicing: ADP-ribose 1"-2" cyclic phosphate." Science 261:206-208.8392224
  • Shull, N. P., Spinelli, S. L., Phizicky, E. M. (2005). "A highly specific phosphatase that acts on ADP-ribose 1''-phosphate, a metabolite of tRNA splicing in Saccharomyces cerevisiae." Nucleic Acids Res 33:650-660.15684411
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDHMDB11671
Pubchem Compound ID44415073
Kegg IDNot Available
ChemSpider ID23106974
FOODB IDFDB025209
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. tRNA 2'-phosphotransferase
General function:
Involved in transferase activity, transferring phosphorus-containing groups
Specific function:
Catalyzes the last step of tRNA splicing, the transfer of the splice junction 2'-phosphate from ligated tRNA to NAD to produce ADP-ribose 1''-2'' cyclic phosphate
Gene Name:
TPT1
Uniprot ID:
Q12272
Molecular weight:
26196.19922
Reactions
2'-phospho-[ligated tRNA] + NAD(+) → mature tRNA + ADP ribose 1'',2''-phosphate + nicotinamide + H(2)O.