L-Lyxose (ECMDB04097) (M2MDB000608)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)Transporters (5)XML
Proteins (26)
Record Information
Version2.0
Creation Date2012-05-31 14:04:55 -0600
Update Date2015-06-04 18:21:29 -0600
Secondary Accession Numbers
  • ECMDB04097
Identification
Name:L-Lyxose
DescriptionPectin is a heterosaccharide derived from the cell wall of plants. Pectins vary in their chain lengths, complexity and the order of each of the monosaccharide units. The characteristic structure of pectin is a linear chain of alpha(1-4)linked D-galacturonic acid that forms the pectin-backbone, a homogalacturonan.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • (+)-Xylose
  • 2,3,4,5-Tetrahydroxypentanal
  • D-Lyxose
  • DL-Xylose
  • L(+)-Xylose
  • L-Lyxose
  • Lyxose
  • Pectin
  • Pectin sugar
  • Pectinose
  • Pentose
  • Trobicin
Chemical Formula:C6H10O7
Weight:Average: 194.1394
Monoisotopic: 194.042652674
InChI Key:AEMOLEFTQBMNLQ-DTEWXJGMSA-N
InChI:InChI=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
CAS number:9000-69-5
IUPAC Name:(2S,3R,4S,5R,6R)-3,4,5,6-tetrahydroxyoxane-2-carboxylic acid
Traditional IUPAC Name:β-D-galactopyranuronic acid
SMILES:O[C@@H]1O[C@@H]([C@H](O)[C@H](O)[C@H]1O)C(O)=O
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
State:Solid
Charge:-1
Melting point:116 - 121
Experimental Properties:
PropertyValueSource
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:Cytoplasm
Reactions:
L-Lyxose > L-Threo-2-pentulose
L-Lyxose + Water <> Methanol + Pectic acid
SMPDB Pathways:
Starch and sucrose metabolismPW000941 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
  • Amino sugar and nucleotide sugar metabolism ec00520
  • Pentose and glucuronate interconversions ec00040
  • Starch and sucrose metabolism ec00500
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0fvi-3900000000-623cfb10797e088f31a3View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (5 TMS) - 70eV, Positivesplash10-000l-6242950000-7b610ed98440b47c2a32View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-00kr-6900000000-a4a0a279e2e16f432677View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-000i-9100000000-1c90dbe22f830f93ad0fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-004i-9000000000-cefd20d23fb5136d2104View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-002b-0900000000-142e51c19f7b152d18e6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-056s-1900000000-80978d6e9cf43c2a99aeView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4r-9400000000-fe9d58fcfd8f4880243eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0007-2900000000-eecfa94a9428872c9b56View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000w-4900000000-c10f02b5bf83d62924f0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-052f-9200000000-21b195d29543b18b8595View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0002-0900000000-2877a7e6d3ecd32cf172View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000b-7900000000-d748e59637b495442c9eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03dl-9100000000-40ac961f184de816ed86View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0006-3900000000-64f3d0eb26f7bc8ca624View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a73-9300000000-329488f791f643b1c308View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4l-9000000000-474e82a5911096bc3b39View in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Andoh A, Bamba T, Sasaki M: Physiological and anti-inflammatory roles of dietary fiber and butyrate in intestinal functions. JPEN J Parenter Enteral Nutr. 1999 Sep-Oct;23(5 Suppl):S70-3. Pubmed: 10483900
  • Baig MM, Cerda JJ: Pectin: its interaction with serum lipoproteins. Am J Clin Nutr. 1981 Jan;34(1):50-3. Pubmed: 7446458
  • Bosaeus I, Carlsson NG, Sandberg AS, Andersson H: Effect of wheat bran and pectin on bile acid and cholesterol excretion in ileostomy patients. Hum Nutr Clin Nutr. 1986 Nov;40(6):429-40. Pubmed: 3025137
  • Fan TY, Feng QQ, Jia CR, Fan Q, Li CA, Bai XL: Protective effect of Weikang decoction and partial ingredients on model rat with gastric mucosa ulcer. World J Gastroenterol. 2005 Feb 28;11(8):1204-9. Pubmed: 15754406
  • Fleming SE, Marthinsen D, Kuhnlein H: Colonic function and fermentation in men consuming high fiber diets. J Nutr. 1983 Dec;113(12):2535-44. Pubmed: 6317826
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Kelsay JL, Goering HK, Behall KM, Prather ES: Effect of fiber from fruits and vegetables on metabolic responses of human subjects: fiber intakes, fecal excretions, and apparent digestibilities. Am J Clin Nutr. 1981 Sep;34(9):1849-52. Pubmed: 6269418
  • Lairon D, Lafont H, Vigne JL, Nalbone G, Leonardi J, Hauton JC: Effects of dietary fibers and cholestyramine on the activity of pancreatic lipase in vitro. Am J Clin Nutr. 1985 Oct;42(4):629-38. Pubmed: 2996326
  • Levy MC, Edwards-Levy F: Coating alginate beads with cross-linked biopolymers: a novel method based on a transacylation reaction. J Microencapsul. 1996 Mar-Apr;13(2):169-83. Pubmed: 8999122
  • Lewinska D, Rosinski S, Piatkiewicz W: A new pectin-based material for selective LDL-cholesterol removal. Artif Organs. 1994 Mar;18(3):217-22. Pubmed: 8185488
  • Miettinen TA, Tarpila S: Effect of pectin on serum cholesterol, fecal bile acids and biliary lipids in normolipidemic and hyperlipidemic individuals. Clin Chim Acta. 1977 Sep 1;79(2):471-7. Pubmed: 890983
  • Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. Pubmed: 19212411
  • Veldman FJ, Nair CH, Vorster HH, Vermaak WJ, Jerling JC, Oosthuizen W, Venter CS: Possible mechanisms through which dietary pectin influences fibrin network architecture in hypercholesterolaemic subjects. Thromb Res. 1999 Mar 15;93(6):253-64. Pubmed: 10093966
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
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.
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID47954
HMDB IDHMDB03402
Pubchem Compound ID441476
Kegg IDC01508
ChemSpider ID390200
WikipediaL-Lyxose
BioCyc IDPECTIN
EcoCyc IDPECTIN
Ligand ExpoGTR

Enzymes

Protein Details
1. L-rhamnose isomerase
General function:
Involved in L-rhamnose isomerase activity
Specific function:
L-rhamnose = L-rhamnulose
Gene Name:
rhaA
Uniprot ID:
P32170
Molecular weight:
47199
Reactions
L-rhamnose = L-rhamnulose.
Protein Details
2. Putative acyl-CoA thioester hydrolase ybhC
General function:
Involved in pectinesterase activity
Specific function:
Putative thioesterase. Does not bind pectin, and has no pectinesterase activity
Gene Name:
ybhC
Uniprot ID:
P46130
Molecular weight:
46082

Transporters

Protein Details
1. Outer membrane protein N
General function:
Involved in transporter activity
Specific function:
Non-specific porin
Gene Name:
ompN
Uniprot ID:
P77747
Molecular weight:
41220
Protein Details
2. Outer membrane pore protein E
General function:
Involved in transporter activity
Specific function:
Uptake of inorganic phosphate, phosphorylated compounds, and some other negatively charged solutes
Gene Name:
phoE
Uniprot ID:
P02932
Molecular weight:
38922
Protein Details
3. L-rhamnose-proton symporter
General function:
Involved in rhamnose transmembrane transporter activity
Specific function:
Uptake of L-rhamnose across the boundary membrane with the concomitant transport of protons into the cell (symport system). Can also transport L-mannose and L-xylose, but at reduced rates
Gene Name:
rhaT
Uniprot ID:
P27125
Molecular weight:
37319
Protein Details
4. Outer membrane protein F
General function:
Involved in transporter activity
Specific function:
OmpF is a porin that forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane. It is also a receptor for the bacteriophage T2
Gene Name:
ompF
Uniprot ID:
P02931
Molecular weight:
39333
Protein Details
5. Outer membrane protein C
General function:
Involved in transporter activity
Specific function:
Forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane
Gene Name:
ompC
Uniprot ID:
P06996
Molecular weight:
40368