ECMDB: L-Threo-2-pentulose (ECMDB00751) (M2MDB000183)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (6)Transporters (7)XML

Proteins (136)

Record Information

Version

2.0

Creation Date

2012-05-31 13:01:01 -0600

Update Date

2015-06-03 15:53:35 -0600

Secondary Accession Numbers

ECMDB00751

Identification

Name:

L-Threo-2-pentulose

Description

L-Threo-2-pentulose, also called L-xylulose, is a ketopentose - a monosaccharide containing five carbon atoms, and including a ketone functional group. It has chemical formula C5H10O5. In nature it occurs in the L- and D- isomers. (Wikipedia)

Structure

MOL SDF PDB SMILES InChI

Synonyms:

L-Xylulose

Chemical Formula:

C₅H₁₀O₅

Weight:

Average: 150.1299
Monoisotopic: 150.05282343

InChI Key:

ZAQJHHRNXZUBTE-WVZVXSGGSA-N

InChI:

InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h3,5-8,10H,1-2H2/t3-,5+/m0/s1

CAS number:

527-50-4

IUPAC Name:

(3R,4S)-1,3,4,5-tetrahydroxypentan-2-one

Traditional IUPAC Name:

xylulose

SMILES:

OC[C@H](O)[C@@H](O)C(=O)CO

Chemical Taxonomy

Description

belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

Alternative Parents

Substituents

Pentose monosaccharide
Beta-hydroxy ketone
Acyloin
Alpha-hydroxy ketone
Secondary alcohol
Ketone
Polyol
Organic oxide
Hydrocarbon derivative
Primary alcohol
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

xylulose (CHEBI:17399 )

Physical Properties

State:

Solid

Charge:

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	678 g/L	ALOGPS
logP	-2.2	ALOGPS
logP	-2.6	ChemAxon
logS	0.65	ALOGPS
pKa (Strongest Acidic)	10.57	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	97.99 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	31.6 m³·mol⁻¹	ChemAxon
Polarizability	13.5 Å³	ChemAxon
Number of Rings	0	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:

Adenosine triphosphate + L-Threo-2-pentulose <> ADP + Hydrogen ion + L-Xylulose 5-phosphate
L-Lyxose > L-Threo-2-pentulose
Adenosine triphosphate + L-Threo-2-pentulose <> ADP + L-Xylulose 5-phosphate
Adenosine triphosphate + L-Threo-2-pentulose <> ADP + L-Xylulose 1-phosphate
Adenosine triphosphate + L-Threo-2-pentulose > ADP + L-Xylulose 5-phosphate
L-Threo-2-pentulose + Adenosine triphosphate + L-Threo-2-pentulose > Xylulose 5-phosphate + Adenosine diphosphate + Xylulose 5-phosphate + ADP
β-D-xylopyranose <> L-Threo-2-pentulose
L-Threo-2-pentulose + Adenosine triphosphate > Xylulose 5-phosphate + ADP + Hydrogen ion
L-Threo-2-pentulose + Adenosine triphosphate > L-Xylulose 5-phosphate + ADP + Hydrogen ion
β-L-lyxopyranose <> L-Threo-2-pentulose

SMPDB Pathways:

L-lyxose Degradation	PW002100
Xylose Degradation I	PW002105

KEGG Pathways:

Ascorbate and aldarate metabolism ec00053
Pentose and glucuronate interconversions ec00040

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	splash10-03di-9000000000-5e0dfc74544a16cb6a2b	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positive	splash10-00g3-9127300000-b6aed5448276d0184bc2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-2900000000-3e1ebc07944b3d190ec8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-9300000000-bca65135a1359f774229	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-08fv-9000000000-71ba0bd1388ac4ba066d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000j-9400000000-a8afb4fe5a51e50f0c41	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-052r-9200000000-bbc5e84222a57470dc89	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9000000000-ce9ee9286404da2668c5	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

References

References:

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
Oka H, Suzuki S, Suzuki H, Oda T: Increased urinary excretion of L-xylulose in patients with liver cirrhosis. Clin Chim Acta. 1976 Mar 1;67(2):131-6. Pubmed: 1248150
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:

Ashwell, Gilbert; Kanfer, Julian; Burns, J. J. Mechanism of L-xylulose formation by kidney enzymes. Journal of Biological Chemistry (1959), 234 472-5.

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	17399
HMDB ID	HMDB00751
Pubchem Compound ID	439205
Kegg ID	C00312
ChemSpider ID	20892
Wikipedia ID	Xylulose
BioCyc ID	Not Available

Enzymes

Protein Details

1. Xylose isomerase

General function:: Involved in xylose isomerase activity
Specific function:: D-xylose = D-xylulose
Gene Name:: xylA
Uniprot ID:: P00944
Molecular weight:: 49742

Reactions

D-xylose = D-xylulose.

Protein Details

2. Ribulokinase

General function:: Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:: ATP + L(or D)-ribulose = ADP + L(or D)- ribulose 5-phosphate
Gene Name:: araB
Uniprot ID:: P08204
Molecular weight:: 61089

Reactions

ATP + L(or D)-ribulose = ADP + L(or D)-ribulose 5-phosphate.

Protein Details

3. Xylulose kinase

General function:: Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:: ATP + D-xylulose = ADP + D-xylulose 5- phosphate
Gene Name:: xylB
Uniprot ID:: P09099
Molecular weight:: 52618

Reactions

ATP + D-xylulose = ADP + D-xylulose 5-phosphate.

Protein Details

4. 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

5. Rhamnulokinase

General function:: Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:: ATP + L-rhamnulose = ADP + L-rhamnulose 1- phosphate
Gene Name:: rhaB
Uniprot ID:: P32171
Molecular weight:: 54069

Reactions

ATP + L-rhamnulose = ADP + L-rhamnulose 1-phosphate.

Protein Details

6. L-xylulose/3-keto-L-gulonate kinase

General function:: Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:: Catalyzes the phosphorylation of L-xylulose and 3-keto- L-gulonate. Is involved in L-lyxose utilization via xylulose, and may also be involved in the utilization of 2,3-diketo-L-gulonate
Gene Name:: lyx
Uniprot ID:: P37677
Molecular weight:: 55155

Reactions

ATP + L-xylulose = ADP + L-xylulose 5-phosphate.
ATP + 3-dehydro-L-gulonate = ADP + 3-dehydro-L-gulonate 6-phosphate.

Transporters

Protein Details

1. 2,3-diketo-L-gulonate TRAP transporter small permease protein yiaM

General function:: Carbohydrate transport and metabolism
Specific function:: Part of the tripartite ATP-independent periplasmic (TRAP) transport system yiaMNO involved in the uptake of 2,3- diketo-L-gulonate
Gene Name:: yiaM
Uniprot ID:: P37674
Molecular weight:: 17516

Protein Details

2. 2,3-diketo-L-gulonate TRAP transporter large permease protein yiaN

General function:: Carbohydrate transport and metabolism
Specific function:: Part of the tripartite ATP-independent periplasmic (TRAP) transport system yiaMNO involved in the uptake of 2,3- diketo-L-gulonate
Gene Name:: yiaN
Uniprot ID:: P37675
Molecular weight:: 45368

Protein Details

3. 2,3-diketo-L-gulonate-binding periplasmic protein yiaO

General function:: Involved in transport
Specific function:: Part of the tripartite ATP-independent periplasmic (TRAP) transport system yiaMNO involved in the uptake of 2,3- diketo-L-gulonate. This protein specifically binds 2,3-diketo-L- gulonate. Is not able to bind either L-ascorbate or dehydroascorbate
Gene Name:: yiaO
Uniprot ID:: P37676
Molecular weight:: 35970

Protein Details

4. 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

5. 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

6. 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

7. 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-Threo-2-pentulose (ECMDB00751) (M2MDB000183)

Structure for #<Compound:0xa937d300>

Enzymes

Reactions

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Transporters