ECMDB: Guanosine diphosphate mannose (ECMDB01163) (M2MDB000279)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (4)XML

Proteins (1083)

Record Information

Version

2.0

Creation Date

2012-05-31 13:46:37 -0600

Update Date

2015-06-03 15:53:47 -0600

Secondary Accession Numbers

ECMDB01163

Identification

Name:

Guanosine diphosphate mannose

Description

GDP-mannose is a nucleoside diphosphate sugar that is important in the production of fucosylated oligosaccharides. GDP-mannose is transformed to GDP-fucose via three enzymatic reactions carried out by two proteins, GDP-mannose 4,6-dehydratase (GMD) and a second enzyme, GDP-keto-6-deoxymannose 3,5-epimerase, 4-reductase. GDP-mannose 4,6-dehydratase (EC 4.2.1.47) catalyzes the chemical reaction: GDP-mannose <--> GDP-4-dehydro-6-deoxy-D-mannose + H2O. The epimerase converts the GDP-4-dehydro-6-deoxy-D-mannose to GDP-fucose. (PMID: 12651883). GDP-mannose is also synthesized from mannose 1-phosphate via the enzyme ATP-mannose-1-phosphate-guanyltransferase and GTP.

Structure

MOL SDF PDB SMILES InChI

Synonyms:

GDP Mannose
GDP-D-Mannose
GDP-Glucose
GDP-Man
GDP-Mannose
GDP-α-D-mannose
Guanosine Diphosphate Mannose
Guanosine diphosphomannose
Guanosine diphosphoric acid mannose
Guanosine pyrophosphate mannose
Guanosine pyrophosphoric acid mannose

Chemical Formula:

C₁₆H₂₅N₅O₁₆P₂

Weight:

Average: 605.3411
Monoisotopic: 605.077152801

InChI Key:

MVMSCBBUIHUTGJ-GDJBGNAASA-N

InChI:

InChI=1S/C16H25N5O16P2/c17-16-19-12-6(13(28)20-16)18-3-21(12)14-10(26)8(24)5(34-14)2-33-38(29,30)37-39(31,32)36-15-11(27)9(25)7(23)4(1-22)35-15/h3-5,7-11,14-15,22-27H,1-2H2,(H,29,30)(H,31,32)(H3,17,19,20,28)/t4-,5-,7-,8-,9+,10-,11+,14-,15-/m1/s1

CAS number:

3123-67-9

IUPAC Name:

[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]({[(2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})phosphinic acid

Traditional IUPAC Name:

guanosine diphosphomannose

SMILES:

NC1=NC2=C(N=CN2[C@@H]2O[C@H](COP(O)(=O)OP(O)(=O)O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O)[C@@H](O)[C@H]2O)C(=O)N1

Chemical Taxonomy

Description

belongs to the class of organic compounds known as purine nucleotide sugars. These are purine nucleotides bound to a saccharide derivative through the terminal phosphate group.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine nucleotide sugars

Direct Parent

Purine nucleotide sugars

Alternative Parents

Substituents

Purine nucleotide sugar
Purine ribonucleoside diphosphate
Purine ribonucleoside monophosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Organic pyrophosphate
Imidazopyrimidine
Purine
Hydroxypyrimidine
Monoalkyl phosphate
Monosaccharide
N-substituted imidazole
Organic phosphoric acid derivative
Oxane
Phosphoric acid ester
Alkyl phosphate
Pyrimidine
Heteroaromatic compound
Tetrahydrofuran
Imidazole
Azole
Secondary alcohol
Polyol
Oxacycle
Organoheterocyclic compound
Azacycle
Organic oxygen compound
Alcohol
Organic oxide
Primary alcohol
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Organic nitrogen compound
Organopnictogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

GDP-D-mannose (CHEBI:15820 )

Physical Properties

State:

Solid

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	7.77 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-5.3	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	327.43 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	118.51 m³·mol⁻¹	ChemAxon
Polarizability	48.72 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	0	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:

SMPDB Pathways:

Amino sugar and nucleotide sugar metabolism II	PW000887
Mannose Metabolism	PW000822
colanic acid building blocks biosynthesis	PW000951

KEGG Pathways:

Amino sugar and nucleotide sugar metabolism ec00520
Ascorbate and aldarate metabolism ec00053
Fructose and mannose metabolism ec00051
Metabolic pathways eco01100

EcoCyc Pathways:

GDP-L-fucose biosynthesis I (from GDP-D-mannose) PWY-66
GDP-mannose biosynthesis PWY-5659

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-05bu-5842490000-d73f755e03b8ad234b29	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-01r6-7882509000-02adbc06a0f79e803d88	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_8) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_9) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_10) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_12) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_13) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_14) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 32V, positive	splash10-0a4i-0000209000-fa2b35ba4f2fbdff74a3	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 32V, negative	splash10-0udi-3401309000-93213e14894fde4ba5c2	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-0001309000-586a7f020650fe518e5f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-0900000000-bba5489b865ff8d5ba78	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-0006-0100900000-d5b51af9c9e096503197	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0900400000-3410bfae1c82b5e08999	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-00b9-9434300000-661dad8f3e9cd9b10a38	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0000009000-c84788b57e1d68c3a299	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0910510000-30a5518df6f0f53ad7b7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0910000000-48aef418f3aa94cc35f8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-1900000000-438261daf883fac47d6c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-1901325000-e5d0bcd5db4a59b606f8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-1901100000-a8c00836fd0ca5a71ad1	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0pdl-3900000000-358726d071759c859d9e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0000009000-3f663b5fce4f431e1e25	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-4701986000-bb5e3a66be23d7de55e6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-05i0-3911810000-ee275d8a12bcf1e5065c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0900002000-37d2f661727ecc1c915a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0900001000-de8f3c7c7e6a620f0e90	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udr-2930000000-7a0fc600f843201b86c4	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:

Becker, D. J., Lowe, J. B. (2003). "Fucose: biosynthesis and biological function in mammals." Glycobiology 13:41R-53R. Pubmed: 12651883
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
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
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:

Huang, Gang-Liang; Liu, Xiang; Zhang, Hou-Cheng; Wang, Peng-George. A facile two-step chemo-enzymatic synthesis of GDP-mannose. Letters in Organic Chemistry (2006), 3(9), 668-669.

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	15820
HMDB ID	HMDB01163
Pubchem Compound ID	732
Kegg ID	C00096
ChemSpider ID	17372
Wikipedia	Guanosine diphosphate mannose
BioCyc ID	GDP-MANNOSE
EcoCyc ID	GDP-MANNOSE
Ligand Expo	GDD

Enzymes

Protein Details

1. GDP-mannose 4,6-dehydratase

General function:: Involved in catalytic activity
Specific function:: GDP-mannose = GDP-4-dehydro-6-deoxy-D-mannose + H(2)O
Gene Name:: gmd
Uniprot ID:: P0AC88
Molecular weight:: 42047

Reactions

GDP-mannose = GDP-4-dehydro-6-deoxy-D-mannose + H(2)O.

Protein Details

2. Mannose-1-phosphate guanylyltransferase

General function:: Involved in nucleotidyltransferase activity
Specific function:: Involved in the biosynthesis of the capsular polysaccharide colanic acid
Gene Name:: manC
Uniprot ID:: P24174
Molecular weight:: 53016

Reactions

GTP + alpha-D-mannose 1-phosphate = diphosphate + GDP-mannose.

Protein Details

3. GDP-mannose mannosyl hydrolase

General function:: Involved in hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
Specific function:: Could participate in the regulation of cell wall biosynthesis by influencing the concentration of GDP-mannose or GDP-glucose in the cell. May be involved in the degradation of GDP-mannose and GDP-glucose, diverting the GDP to the synthesis of GDP-fucose as required. Might also be involved in the biosynthesis of the slime polysaccharide colanic acid
Gene Name:: nudD
Uniprot ID:: P32056
Molecular weight:: 18273

Reactions

GDP-D-mannose + H(2)O = GDP + D-mannose.

Protein Details

4. GDP-mannose pyrophosphatase nudK

General function:: Involved in hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
Specific function:: Catalyzes the hydrolysis of GDP-mannose. Can also use other substrates, catalyzing the hydrolysis of the pyrophosphate bond, releasing a nucleoside monophosphate and a phosphorylated moiety, depending on the substrate
Gene Name:: nudK
Uniprot ID:: P37128
Molecular weight:: 21749

Reactions

GDP-mannose + H(2)O = GMP + mannose-1-phosphate.

Guanosine diphosphate mannose (ECMDB01163) (M2MDB000279)

Structure for #<Compound:0xa65c8ab8>

Enzymes

Reactions

Reactions

Reactions

Reactions