You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.
Identification
YMDB IDYMDB00904
NamePectin
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionPectin, also known as galacturonate or D-lyxose, belongs to the class of organic compounds known as glucuronic acid derivatives. Glucuronic acid derivatives are compounds containing a glucuronic acid moiety (or a derivative), which consists of a glucose moiety with the C6 carbon oxidized to a carboxylic acid. Pectin is an extremely weak basic (essentially neutral) compound (based on its pKa). Pectin exists in all living species, ranging from bacteria to humans.
Structure
Thumb
Synonyms
  • (+)-Xylose
  • 2,3,4,5-Tetrahydroxypentanal
  • D-Lyxose
  • DL-Xylose
  • L-Lyxose
  • L(+)-Xylose
  • Lyxose
  • Pectin
  • Pectin sugar
  • Pectinose
  • Pentose
  • Trobicin
  • Pectinic acid
  • Calcium pectinate
  • Methoxy pectin
  • Methoxylpectin
  • Methoxypectin
  • Zinc pectinate
  • Galacturonate
  • b-D-Galacturonate
  • b-D-Galacturonic acid
  • beta-D-Galacturonate
  • Β-D-galacturonate
  • Β-D-galacturonic acid
CAS number9000-69-5
WeightAverage: 194.1394
Monoisotopic: 194.042652674
InChI KeyAEMOLEFTQBMNLQ-DTEWXJGMSA-N
InChIInChI=1S/C6H10O7/c7-1-2(8)4(5(10)11)13-6(12)3(1)9/h1-4,6-9,12H,(H,10,11)/t1-,2+,3+,4-,6+/m0/s1
IUPAC Name(2S,3R,4S,5R,6R)-3,4,5,6-tetrahydroxyoxane-2-carboxylic acid
Traditional IUPAC Nameβ-D-galactopyranuronic acid
Chemical FormulaC6H10O7
SMILES[H]OC(=O)[C@@]1([H])O[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@@]1([H])O[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as glucuronic acid derivatives. Glucuronic acid derivatives are compounds containing a glucuronic acid moiety (or a derivative), which consists of a glucose moiety with the C6 carbon oxidized to a carboxylic acid.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentGlucuronic acid derivatives
Alternative Parents
Substituents
  • Glucuronic acid or derivatives
  • Beta-hydroxy acid
  • Hydroxy acid
  • Pyran
  • Monosaccharide
  • Oxane
  • Hemiacetal
  • Secondary alcohol
  • Carboxylic acid derivative
  • Carboxylic acid
  • Oxacycle
  • Organoheterocyclic compound
  • Monocarboxylic acid or derivatives
  • Polyol
  • Hydrocarbon derivative
  • Organic oxide
  • Carbonyl group
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility295 g/LALOGPS
logP-2.3ALOGPS
logP-2.6ChemAxon
logS0.18ALOGPS
pKa (Strongest Acidic)3.21ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area127.45 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity35.79 m³·mol⁻¹ChemAxon
Polarizability16.37 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • extracellular
Organoleptic PropertiesNot Available
SMPDB Pathways
Amino sugar and nucleotide sugar metabolismPW002413 ThumbThumb?image type=greyscaleThumb?image type=simple
Starch and sucrose metabolismPW002481 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Amino sugar and nucleotide sugar metabolismec00520 Map00520
Pentose and glucuronate interconversionsec00040 Map00040
Starch and sucrose metabolismec00500 Map00500
SMPDB ReactionsNot Available
KEGG Reactions
water + Pectin aldehydo-D-galacturonate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0fvi-3900000000-623cfb10797e088f31a3JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (5 TMS) - 70eV, Positivesplash10-000l-6242950000-7b610ed98440b47c2a32JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-00kr-6900000000-a4a0a279e2e16f432677JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-000i-9100000000-1c90dbe22f830f93ad0fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-004i-9000000000-cefd20d23fb5136d2104JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-002b-0900000000-142e51c19f7b152d18e6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-056s-1900000000-80978d6e9cf43c2a99aeJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4r-9400000000-fe9d58fcfd8f4880243eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0007-2900000000-eecfa94a9428872c9b56JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000w-4900000000-c10f02b5bf83d62924f0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-052f-9200000000-21b195d29543b18b8595JSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • 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
  • Louw, C., Young, P. R., van Rensburg, P., Divol, B. (2010). "Regulation of endo-polygalacturonase activity in Saccharomyces cerevisiae." FEMS Yeast Res 10:44-57.19840115
Synthesis Reference:Gu, Qu-Ming; Nickol, Robert G.; Cheng, H. N. Enzyme-catalyzed modification of pectin. Polymer Preprints (American Chemical Society, Division of Polymer Chemistry) (2003), 44(2), 608-609.
External Links:
ResourceLink
CHEBI ID17309
HMDB IDHMDB03402
Pubchem Compound ID854
Kegg IDC00714
ChemSpider ID25084799
FOODB IDFDB023162
WikipediaPectin
BioCyc IDPECTIN

Enzymes

General function:
Involved in polygalacturonase activity
Specific function:
Random hydrolysis of (1->4)-alpha-D- galactosiduronic linkages in pectate and other galacturonans
Gene Name:
PGU1
Uniprot ID:
P47180
Molecular weight:
37286.60156
Reactions