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Identification
YMDB IDYMDB00257
NameGuanosine diphosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionGuanosine diphosphate, also known as 5'-GDP or 5'-diphosphate, guanosine, belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety. Guanosine diphosphate is a moderately basic compound (based on its pKa). Guanosine diphosphate exists in all living species, ranging from bacteria to humans. In yeast, guanosine diphosphate is involved in the metabolic pathway called n-glycan biosynthesis pathway.
Structure
Thumb
Synonyms
  • 5'-GDP
  • GDP
  • Guanosine 5'-(trihydrogen pyrophosphate)
  • Guanosine 5'-diphosphate
  • Guanosine 5'-pyrophosphate
  • Guanosine mono(trihydrogen diphosphate)
  • Guanosine pyrophosphate
  • guanosine-5'-diphosphate
  • guanosine-diphosphate
  • ppG
  • Guanosine 5'-diphosphoric acid
  • Guanosine diphosphoric acid
  • 5'-Diphosphate, guanosine
  • Diphosphate, guanosine 5'-trihydrogen
  • Guanosine 5' diphosphate
  • Guanosine 5' trihydrogen diphosphate
  • 5'-Trihydrogen diphosphate, guanosine
  • Diphosphate, guanosine
  • Guanosine 5'-trihydrogen diphosphate
CAS number146-91-8
WeightAverage: 443.2005
Monoisotopic: 443.024329371
InChI KeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
IUPAC Name[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-6,9-dihydro-3H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional IUPAC Name{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-3H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid
Chemical FormulaC10H15N5O11P2
SMILES[H]O[C@]1([H])[C@]([H])(O[H])[C@]([H])(O[C@@]1([H])N1C([H])=NC2=C1N=C(N([H])[H])N([H])C2=O)C([H])([H])OP(=O)(O[H])OP(=O)(O[H])O[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleotides
Sub ClassPurine ribonucleotides
Direct ParentPurine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Purine ribonucleoside diphosphate
  • Purine ribonucleoside monophosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • 6-oxopurine
  • Hypoxanthine
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Pentose monosaccharide
  • Imidazopyrimidine
  • Purine
  • Aminopyrimidine
  • Monoalkyl phosphate
  • Pyrimidone
  • Monosaccharide
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Alkyl phosphate
  • Phosphoric acid ester
  • Pyrimidine
  • Vinylogous amide
  • Tetrahydrofuran
  • Azole
  • Imidazole
  • Heteroaromatic compound
  • Secondary alcohol
  • 1,2-diol
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Organooxygen compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Alcohol
  • Amine
  • Organic oxygen compound
  • Primary amine
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility4.46 g/LALOGPS
logP-1.5ALOGPS
logP-3.7ChemAxon
logS-2ALOGPS
pKa (Strongest Acidic)1.71ChemAxon
pKa (Strongest Basic)2.55ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area248.28 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity85.93 m³·mol⁻¹ChemAxon
Polarizability34.74 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • Golgi
  • mitochondrion
  • nucleus
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Citric Acid CyclePW000952 ThumbThumb?image type=greyscaleThumb?image type=simple
Citric Acid Cycle 1434561204PW000970 ThumbThumb?image type=greyscaleThumb?image type=simple
Mannose MetabolismPW002391 ThumbThumb?image type=greyscaleThumb?image type=simple
N-Glycan biosynthesisPW002501 ThumbThumb?image type=greyscaleThumb?image type=simple
TCA CyclePW002377 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
N-Glycan biosynthesisec00510 Map00510
Purine metabolismec00230 Map00230
SMPDB Reactions
Succinyl-CoA + phosphate + Guanosine diphosphateSuccinic acid + Coenzyme A + GTP
GTP + Inosinic acid + L-Aspartic acidGuanosine diphosphate + phosphate + Adenylsuccinic acid
Inosinic acid + L-Aspartic acid + GTPGuanosine diphosphate + phosphate + hydron + N6-(1,2-Dicarboxyethyl)-AMP
Guanosine diphosphate + Adenosine triphosphateADP + GTP
Guanosine diphosphate + reduced thioredoxin → oxidized thioredoxin + water + dGDP
KEGG Reactions
Adenosine monophosphate + GTPADP + Guanosine diphosphate
GTP + Inosinic acid + L-Aspartic acidphosphate + hydron + Guanosine diphosphate + Adenylsuccinic acid
Beta-1,4-D-Mannosylchitobiosyldiphosphodolichol + Guanosine diphosphate mannosealpha-D-mannosyl-beta-D-mannosyldiacetylchitobiosyldiphosphodolichol + hydron + Guanosine diphosphate
GTP + hydron + Guanosine diphosphatephosphate + P(1),P(4)-bis(5'-guanosyl) tetraphosphate
GTP + CytidineCytidine monophosphate + hydron + Guanosine diphosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • 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
  • Romero, P. A., Lussier, M., Sdicu, A. M., Bussey, H., Herscovics, A. (1997). "Ktr1p is an alpha-1,2-mannosyltransferase of Saccharomyces cerevisiae. Comparison of the enzymic properties of soluble recombinant Ktr1p and Kre2p/Mnt1p produced in Pichia pastoris." Biochem J 321 ( Pt 2):289-295.9020857
  • Vozza, A., Blanco, E., Palmieri, L., Palmieri, F. (2004). "Identification of the mitochondrial GTP/GDP transporter in Saccharomyces cerevisiae." J Biol Chem 279:20850-20857.14998997
  • Lobsanov, Y. D., Romero, P. A., Sleno, B., Yu, B., Yip, P., Herscovics, A., Howell, P. L. (2004). "Structure of Kre2p/Mnt1p: a yeast alpha1,2-mannosyltransferase involved in mannoprotein biosynthesis." J Biol Chem 279:17921-17931.14752117
  • Gao, X. D., Kaigorodov, V., Jigami, Y. (1999). "YND1, a homologue of GDA1, encodes membrane-bound apyrase required for Golgi N- and O-glycosylation in Saccharomyces cerevisiae." J Biol Chem 274:21450-21456.10409709
  • Lussier, M., Sdicu, A. M., Camirand, A., Bussey, H. (1996). "Functional characterization of the YUR1, KTR1, and KTR2 genes as members of the yeast KRE2/MNT1 mannosyltransferase gene family." J Biol Chem 271:11001-11008.8631921
Synthesis Reference:Edlin, Gordon; Donini, P. Synthesis of guanosine 5'-diphosphate, 2'-(or 3'-) diphosphate, and related nucleotides in a variety of physiological conditions. Journal of Biological Chemistry (1971), 246(13), 4371-3.
External Links:
ResourceLink
CHEBI ID17552
HMDB IDHMDB01201
Pubchem Compound ID8977
Kegg IDC00035
ChemSpider ID8630
FOODB IDFDB022487
WikipediaGuanosine_diphosphate
BioCyc IDGDP-4-DEHYDRO-6-DEOXY-D-MANNOSE

Enzymes

General function:
Cell wall/membrane/envelope biogenesis
Specific function:
Transfers mannose from GDP-mannose to dolichol monophosphate to form dolichol phosphate mannose (Dol-P-Man) which is the mannosyl donor in pathways leading to N-glycosylation, glycosyl phosphatidylinositol membrane anchoring, and O- mannosylation of proteins
Gene Name:
DPM1
Uniprot ID:
P14020
Molecular weight:
30362.0
Reactions
GDP-mannose + dolichyl phosphate → GDP + dolichyl D-mannosyl phosphate.
General function:
Involved in ATP adenylyltransferase activity
Specific function:
Ap4A phosphorylase catabolizes Ap4N nucleotides (where N is A,C,G or U). Additionally this enzyme catalyzes the conversion of adenosine-5-phosphosulfate (AMPs) plus Pi to ADP plus sulfate, the exchange of NDP and phosphate and the synthesis of Ap4A from AMPs plus ATP
Gene Name:
APA1
Uniprot ID:
P16550
Molecular weight:
36492.19922
Reactions
ADP + ATP → phosphate + P(1),P(4)-bis(5'-adenosyl) tetraphosphate.
ADP + sulfate → phosphate + adenylyl sulfate.
Adenylylsulfate + ATP → P(1),P(4)-bis(5'-adenosyl)tetraphosphate + sulfate.
General function:
Involved in adenylosuccinate synthase activity
Specific function:
Plays an important role in the de novo pathway and in the salvage pathway of purine nucleotide biosynthesis. Catalyzes the first commited step in the biosynthesis of AMP from IMP
Gene Name:
ADE12
Uniprot ID:
P80210
Molecular weight:
48279.10156
Reactions
GTP + IMP + L-aspartate → GDP + phosphate + N(6)-(1,2-dicarboxyethyl)-AMP.
General function:
Involved in catalytic activity
Specific function:
ATP + succinate + CoA = ADP + phosphate + succinyl-CoA
Gene Name:
LSC1
Uniprot ID:
P53598
Molecular weight:
35032.19922
Reactions
ATP + succinate + CoA → ADP + phosphate + succinyl-CoA.
General function:
Involved in catalytic activity
Specific function:
ATP + succinate + CoA = ADP + phosphate + succinyl-CoA
Gene Name:
LSC2
Uniprot ID:
P53312
Molecular weight:
46900.30078
Reactions
ATP + succinate + CoA → ADP + phosphate + succinyl-CoA.
General function:
Involved in hydrolase activity
Specific function:
Catalyzes the hydrolysis of phosphoanhydride bonds of nucleoside tri- and di-phosphates. Has equal high activity toward ADP/ATP, GDP/GTP, and UDP/UTP and approximately 50% less toward CDP/CTP and thiamine pyrophosphate. Has no activity toward GMP. Required for Golgi glycosylation and cell wall integrity. Together with CDC55, required for adenovirus E4orf4 (early region 4 open reading frame 4) induced toxicity, the apyrase activity is not required for this function. Plays a role in sphingolipid synthesis
Gene Name:
YND1
Uniprot ID:
P40009
Molecular weight:
71851.20313
Reactions
ATP + 2 H(2)O → AMP + 2 phosphate.
General function:
Involved in ATP binding
Specific function:
Catalyzes the conversion of uridine into UMP and cytidine into CMP in the pyrimidine salvage pathway
Gene Name:
URK1
Uniprot ID:
P27515
Molecular weight:
56295.5
Reactions
ATP + uridine → ADP + UMP.
ATP + cytidine → ADP + CMP.
General function:
Involved in oxidoreductase activity
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. RNR2 provides the diiron-tyrosyl radical center
Gene Name:
RNR2
Uniprot ID:
P09938
Molecular weight:
46147.0
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O → ribonucleoside diphosphate + thioredoxin.
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. Required for repair of UV radiation- and etoposide-induced DNA damage
Gene Name:
YNK1
Uniprot ID:
P36010
Molecular weight:
17166.59961
Reactions
ATP + nucleoside diphosphate → ADP + nucleoside triphosphate.
General function:
Involved in oxidation-reduction process
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
Gene Name:
RNR1
Uniprot ID:
P21524
Molecular weight:
99560.20313
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O → ribonucleoside diphosphate + thioredoxin.
General function:
Involved in ATP binding
Specific function:
RAR (regulation of autonomous replication) is a protein whose activity increases the mitotic stability of plasmids
Gene Name:
ERG12
Uniprot ID:
P07277
Molecular weight:
48458.89844
Reactions
ATP + (R)-mevalonate → ADP + (R)-5-phosphomevalonate.
General function:
Involved in ATP binding
Specific function:
This small ubiquitous enzyme is essential for maintenance and cell growth
Gene Name:
ADK2
Uniprot ID:
P26364
Molecular weight:
25193.69922
Reactions
ATP + AMP → 2 ADP.
General function:
Involved in ATP binding
Specific function:
Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Small ubiquitous enzyme involved in energy metabolism and nucleotide synthesis that is essential for maintenance and cell growth. Functions both in the cytoplasm and mitochondrion intermembrane space
Gene Name:
ADK1
Uniprot ID:
P07170
Molecular weight:
24254.5
Reactions
ATP + AMP → 2 ADP.
General function:
Involved in protein binding
Specific function:
Essential for recycling GMP and indirectly, cGMP
Gene Name:
GUK1
Uniprot ID:
P15454
Molecular weight:
20637.19922
Reactions
ATP + GMP → ADP + GDP.
General function:
Involved in biosynthetic process
Specific function:
Participates in the formation of the lipid-linked precursor oligosaccharide for N-glycosylation. Involved in assembling the dolichol-pyrophosphate-GlcNAc(2)-Man(5) intermediate on the cytoplasmic surface of the ER
Gene Name:
ALG1
Uniprot ID:
P16661
Molecular weight:
51928.5
Reactions
GDP-mannose + chitobiosyldiphosphodolichol → GDP + beta-1,4-D-mannosylchitobiosyldiphosphodolichol.
General function:
Involved in mannosyltransferase activity
Specific function:
Required for the attachment of the third mannose residue of O-linked saccharides
Gene Name:
KRE2
Uniprot ID:
P27809
Molecular weight:
51386.19922
Reactions
General function:
Involved in mannosyltransferase activity
Specific function:
Mannosyltransferase that transfers a mannose residue from GDP-mannose to a range of acceptors in vitro
Gene Name:
KTR1
Uniprot ID:
P27810
Molecular weight:
46021.69922
Reactions
General function:
Involved in mannosyltransferase activity
Specific function:
Involved in N-linked glycosylation
Gene Name:
KTR2
Uniprot ID:
P33550
Molecular weight:
50650.89844
Reactions
General function:
Involved in mannosyltransferase activity
Specific function:
Possible glycosyltransferase
Gene Name:
KTR3
Uniprot ID:
P38130
Molecular weight:
47482.0
Reactions
General function:
Involved in mannosyltransferase activity
Specific function:
Possible glycosyltransferase involved in N-linked glycosylation
Gene Name:
YUR1
Uniprot ID:
P26725
Molecular weight:
50835.60156
Reactions
General function:
Involved in oxidoreductase activity
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. RNR4 is required for proper folding of RNR2 and assembly with the large subunits
Gene Name:
RNR4
Uniprot ID:
P49723
Molecular weight:
40054.19922
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O → ribonucleoside diphosphate + thioredoxin.
General function:
Involved in hydrolase activity
Specific function:
After transfer of sugars to endogenous macromolecular acceptors, the enzyme converts nucleoside diphosphates to nucleoside monophosphates which in turn exit the Golgi lumen in a coupled antiporter reaction, allowing entry of additional nucleotide sugar from the cytosol
Gene Name:
GDA1
Uniprot ID:
P32621
Molecular weight:
56821.0
Reactions
GDP + H(2)O → GMP + phosphate.
General function:
Cell wall/membrane/envelope biogenesis
Specific function:
Mannosylates Man(2)GlcNAc(2)-dolichol diphosphate and Man(1)GlcNAc(2)-dolichol diphosphate to form Man(3)GlcNAc(2)- dolichol diphosphate
Gene Name:
ALG2
Uniprot ID:
P43636
Molecular weight:
58046.5
Reactions
General function:
Involved in oxidation-reduction process
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
Gene Name:
RNR3
Uniprot ID:
P21672
Molecular weight:
97513.79688
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O → ribonucleoside diphosphate + thioredoxin.
General function:
protein glycosylation
Specific function:
Required for N-linked oligosaccharide assembly. Has a role in the last step of the synthesis of the Man(5)GlcNAc(2)-PP-dolichol core oligosaccharide on the cytoplasmic face of the endoplasmic reticulum.
Gene Name:
ALG11
Uniprot ID:
P53954
Molecular weight:
63142.705
Reactions

Transporters

General function:
Involved in guanine nucleotide transmembrane transporte
Specific function:
Not Available
Gene Name:
YHM1
Uniprot ID:
P38988
Molecular weight:
33215.19922