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N,N'-diacetylchitobiosyldiphosphodolichol (YMDB00940)

Identification
YMDB IDYMDB00940
NameN,N'-diacetylchitobiosyldiphosphodolichol
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionN,N'-Diacetylchitobiosyldiphosphodolichol is involved in dolichyl-diphosphooligosaccharide biosynthesis (N-linked glycosylation) pathway. N-linked glycosylation is an important process found in eukaryotes and archaea, and very rarely in bacteria. During this process certain oligosaccharides are attached to an asparagine residue in the polypeptide chain of the target protein. [Biocyc MANNOSYL-CHITO-DOLICHOL-BIOSYNTHESIS]
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • Chitobiosyldiphosphodolichol
  • N,N'-Diacetylchitobiosyldiphosphodolichol
CAS numberNot Available
WeightAverage: 1948.7164
Monoisotopic: 1947.369625752
InChI KeyPRYYLPDTMLHFQH-RJSWRCNLSA-N
InChIInChI=1S/C116H192N2O17P2/c1-85(2)43-24-44-86(3)45-25-46-87(4)47-26-48-88(5)49-27-50-89(6)51-28-52-90(7)53-29-54-91(8)55-30-56-92(9)57-31-58-93(10)59-32-60-94(11)61-33-62-95(12)63-34-64-96(13)65-35-66-97(14)67-36-68-98(15)69-37-70-99(16)71-38-72-100(17)73-39-74-101(18)75-40-76-102(19)77-41-78-103(20)79-42-80-104(21)81-82-130-136(126,127)135-137(128,129)134-116-110(118-106(23)122)113(125)114(108(84-120)132-116)133-115-109(117-105(22)121)112(124)111(123)107(83-119)131-115/h43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,79,104,107-116,119-120,123-125H,24-42,44,46,48,50,52,54,56,58,60,62,64,66,68,70,72,74,76,78,80-84H2,1-23H3,(H,117,121)(H,118,122)(H,126,127)(H,128,129)/b86-45+,87-47+,88-49+,89-51+,90-53-,91-55+,92-57+,93-59+,94-61+,95-63+,96-65+,97-67+,98-69+,99-71-,100-73+,101-75+,102-77+,103-79+/t104?,107-,108-,109-,110-,111-,112-,113-,114-,115+,116-/m1/s1
IUPAC Name{[(2R,3R,4R,5S,6R)-3-acetamido-5-{[(2S,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}({[hydroxy({[(6E,10E,14E,18E,22Z,26E,30E,34E,38E,42E,46E,50E,54E,58Z,62E,66E,70E,74E)-3,7,11,15,19,23,27,31,35,39,43,47,51,55,59,63,67,71,75,79-icosamethyloctaconta-6,10,14,18,22,26,30,34,38,42,46,50,54,58,62,66,70,74,78-nonadecaen-1-yl]oxy})phosphoryl]oxy})phosphinic acid
Traditional IUPAC Name[(2R,3R,4R,5S,6R)-3-acetamido-5-{[(2S,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy({hydroxy[(6E,10E,14E,18E,22Z,26E,30E,34E,38E,42E,46E,50E,54E,58Z,62E,66E,70E,74E)-3,7,11,15,19,23,27,31,35,39,43,47,51,55,59,63,67,71,75,79-icosamethyloctaconta-6,10,14,18,22,26,30,34,38,42,46,50,54,58,62,66,70,74,78-nonadecaen-1-yl]oxyphosphoryl}oxy)phosphinic acid
Chemical FormulaC116H192N2O17P2
SMILESOC[C@H]1O[C@@H](O[C@H]2[C@H](O)[C@@H](NC(=O)C)[C@H](O[C@@H]2CO)OP(O)(=O)OP(O)(=O)OCCC(C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(\C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(\C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CCC=C(C)C)[C@H](NC(=O)C)[C@@H](O)[C@@H]1O
Chemical Taxonomy
Description belongs to the class of organic compounds known as polyprenyl phospho carbohydrates. These are polyprenyl phosphates with a carbohydrate moiety attached to it.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassPolyprenols
Direct ParentPolyprenyl phospho carbohydrates
Alternative Parents
Substituents
  • Polyprenyl phospho oligosaccharide
  • Polyterpenoid
  • Polyprenyl phospho carbohydrate
  • Dolichyl diphosphate
  • Polyprenyl monophosphate
  • Polyprenyl phosphate skeleton
  • N-acyl-alpha-hexosamine
  • Disaccharide phosphate
  • O-glycosyl compound
  • Glycosyl compound
  • Disaccharide
  • Organic pyrophosphate
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Oxane
  • Organic phosphoric acid derivative
  • Acetamide
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Carboxamide group
  • Oxacycle
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Acetal
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.00081 g/LALOGPS
logP8.5ALOGPS
logP27.7ChemAxon
logS-6.4ALOGPS
pKa (Strongest Acidic)1.74ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count14ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area289.33 ŲChemAxon
Rotatable Bond Count71ChemAxon
Refractivity587.44 m³·mol⁻¹ChemAxon
Polarizability236.02 ųChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB PathwaysNot Available
KEGG PathwaysNot Available
SMPDB ReactionsNot Available
KEGG Reactions
Guanosine diphosphate mannose + N,N'-diacetylchitobiosyldiphosphodolichol ↔ Beta-1,4-D-Mannosylchitobiosyldiphosphodolichol
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • 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
  • Burda, P., Aebi, M. (1999). "The dolichol pathway of N-linked glycosylation." Biochim Biophys Acta 1426:239-257.9878760
  • Huh, W. K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S., O'Shea, E. K. (2003). "Global analysis of protein localization in budding yeast." Nature 425:686-691.14562095
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID12427
HMDB IDHMDB01196
Pubchem Compound ID440378
Kegg IDC04537
ChemSpider IDNot Available
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc IDNN-DIACETYLCHITOBIOSYLDIPHOSPHODOLICHO

Enzymes

Protein Details
1. Chitobiosyldiphosphodolichol beta-mannosyltransferase
General function:
Involved in biosynthetic process
Specific function:
Participates in the formation of the lipid-linked precursor oligosaccharide for N-glycosylation. Involved in assembling the dolichol-pyrophosphate-GlcNAc(2)-Man(5) intermediate on the cytoplasmic surface of the ER
Gene Name:
ALG1
Uniprot ID:
P16661
Molecular weight:
51928.5
Reactions
GDP-mannose + chitobiosyldiphosphodolichol → GDP + beta-1,4-D-mannosylchitobiosyldiphosphodolichol.