Pectin (YMDB00904)

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
MOLSDFPDBSMILESInChI
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
  • b-D-Galactopyranuronate
  • b-D-Galactopyranuronic acid
  • beta-D-Galactopyranuronate
  • Β-D-galactopyranuronate
  • Β-D-galactopyranuronic 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
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
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
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0002-0900000000-2877a7e6d3ecd32cf172JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000b-7900000000-d748e59637b495442c9eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03dl-9100000000-40ac961f184de816ed86JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0006-3900000000-64f3d0eb26f7bc8ca624JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a73-9300000000-329488f791f643b1c308JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4l-9000000000-474e82a5911096bc3b39JSpectraViewer
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
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

Protein Details
1. Polygalacturonase
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