ECMDB: L-Lyxose (ECMDB04097) (M2MDB000608)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (2)Transporters (5)XML

Proteins (26)

Record Information

Version

2.0

Creation Date

2012-05-31 14:04:55 -0600

Update Date

2015-06-04 18:21:29 -0600

Secondary Accession Numbers

ECMDB04097

Identification

Name:

L-Lyxose

Description

Pectin 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

MOL SDF PDB SMILES InChI

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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Glucuronic 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 Framework

Aliphatic heteromonocyclic compounds

External Descriptors

D-galactopyranuronic acid (CHEBI:47954 )

Physical Properties

State:

Solid

Charge:

-1

Melting point:

116 - 121

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	295 g/L	ALOGPS
logP	-2.3	ALOGPS
logP	-2.6	ChemAxon
logS	0.18	ALOGPS
pKa (Strongest Acidic)	3.21	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	127.45 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	35.79 m³·mol⁻¹	ChemAxon
Polarizability	16.37 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

L-Lyxose > L-Threo-2-pentulose
L-Lyxose + Water <> Methanol + Pectic acid

SMPDB Pathways:

Starch and sucrose metabolism

PW000941

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 Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0fvi-3900000000-623cfb10797e088f31a3	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (5 TMS) - 70eV, Positive	splash10-000l-6242950000-7b610ed98440b47c2a32	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-00kr-6900000000-a4a0a279e2e16f432677	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-000i-9100000000-1c90dbe22f830f93ad0f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-004i-9000000000-cefd20d23fb5136d2104	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-002b-0900000000-142e51c19f7b152d18e6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-056s-1900000000-80978d6e9cf43c2a99ae	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4r-9400000000-fe9d58fcfd8f4880243e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0007-2900000000-eecfa94a9428872c9b56	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000w-4900000000-c10f02b5bf83d62924f0	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052f-9200000000-21b195d29543b18b8595	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-0900000000-2877a7e6d3ecd32cf172	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000b-7900000000-d748e59637b495442c9e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03dl-9100000000-40ac961f184de816ed86	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-3900000000-64f3d0eb26f7bc8ca624	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a73-9300000000-329488f791f643b1c308	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9000000000-474e82a5911096bc3b39	View in MoNA
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available	View in JSpectraViewer
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	View 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

Links

External Links:

Resource	Link
CHEBI ID	47954
HMDB ID	HMDB03402
Pubchem Compound ID	441476
Kegg ID	C01508
ChemSpider ID	390200
Wikipedia	L-Lyxose
BioCyc ID	PECTIN
EcoCyc ID	PECTIN
Ligand Expo	GTR

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

L-Lyxose (ECMDB04097) (M2MDB000608)

Structure for #<Compound:0xab2da89c>

Enzymes

Reactions

Transporters