ECMDB: Guanosine 3'-diphosphate 5'-triphosphate (ECMDB20156) (M2MDB001003)

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

Proteins (925)

Record Information

Version

2.0

Creation Date

2012-05-31 14:30:25 -0600

Update Date

2015-06-03 17:19:25 -0600

Secondary Accession Numbers

ECMDB20156

Identification

Name:

Guanosine 3'-diphosphate 5'-triphosphate

Description

Guanosine 3'-diphosphate 5'-triphosphate is a member of the chemical class known as Purine Ribonucleoside 3',5'-Bisphosphates. These are purine ribobucleotides with one phosphate group attached to 3' and 5' hydroxyl groups of the ribose moiety. The hallmark of the stringent response is the accumulation of guanosine tetra- (ppGpp) and pentaphosphates (pppGpp), which probably bind RNA polymerase to regulate gene expression at certain promoters. (PMID 11282471) Guanosine 5'-triphosphate 3'-diphosphate (pppGpp) and guanosine 5'-diphosphate 3'-diphosphate (ppGpp) are specifically degraded by a manganese-dependent pyrophosphorylase present in spoT+ but not in spoT- strains of Escherichia coli, indicating that the enzyme is the spoT gene product. (PMID 365225) The kinetics of the GTP level during starvation suggests that GTP is a precursor of pppGpp. (PMID 793688)

Structure

MOL SDF PDB SMILES InChI

Synonyms:

Guanosine 3'-diphosphate 5'-triphosphate
Guanosine 3'-diphosphoric acid 5'-triphosphoric acid
Guanosine 5'-triphosphate,3'-diphosphate
Guanosine 5'-triphosphoric acid,3'-diphosphoric acid
Guanosine pentaphosphate
Guanosine pentaphosphoric acid
Magic spot
Pppgpp

Chemical Formula:

C₁₀H₁₈N₅O₂₀P₅

Weight:

Average: 683.1402
Monoisotopic: 682.923320601

InChI Key:

KCPMACXZAITQAX-UUOKFMHZSA-N

InChI:

InChI=1S/C10H18N5O20P5/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(32-39(26,27)33-36(18,19)20)3(31-9)1-30-38(24,25)35-40(28,29)34-37(21,22)23/h2-3,5-6,9,16H,1H2,(H,24,25)(H,26,27)(H,28,29)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1

CAS number:

38918-96-6

IUPAC Name:

{[hydroxy({[(2R,3S,4R,5R)-4-hydroxy-2-({[hydroxy({[hydroxy(phosphonooxy)phosphoryl]oxy})phosphoryl]oxy}methyl)-5-(6-hydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)oxolan-3-yl]oxy})phosphoryl]oxy}phosphonic acid

Traditional IUPAC Name:

{hydroxy[(2R,3S,4R,5R)-4-hydroxy-5-(6-hydroxy-2-imino-3H-purin-9-yl)-2-[({hydroxy[hydroxy(phosphonooxy)phosphoryl]oxyphosphoryl}oxy)methyl]oxolan-3-yl]oxyphosphoryl}oxyphosphonic acid

SMILES:

[H][C@]1(COP(O)(=O)OP(O)(=O)OP(O)(O)=O)O[C@@]([H])(N2C=NC3=C2NC(=N)N=C3O)[C@]([H])(O)[C@]1([H])OP(O)(=O)OP(O)(O)=O

Chemical Taxonomy

Description

belongs to the class of organic compounds known as purine ribonucleoside triphosphates. These are purine ribobucleotides with a triphosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine ribonucleotides

Direct Parent

Purine ribonucleoside triphosphates

Alternative Parents

Substituents

Purine ribonucleoside triphosphate
Purine ribonucleoside 3',5'-bisphosphate
Purine ribonucleoside bisphosphate
Ribonucleoside 3'-phosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
6-oxopurine
Hypoxanthine
Monosaccharide phosphate
Organic pyrophosphate
Imidazopyrimidine
Purine
Aminopyrimidine
Monoalkyl phosphate
Pyrimidone
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Monosaccharide
N-substituted imidazole
Organic phosphoric acid derivative
Tetrahydrofuran
Vinylogous amide
Azole
Imidazole
Heteroaromatic compound
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Hydrocarbon derivative
Amine
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Primary amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

guanosine 5'-phosphate (CHEBI:16690 )
guanosine bisphosphate (CHEBI:16690 )

Physical Properties

State:

Not Available

Charge:

-6

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	16.8 g/L	ALOGPS
logP	0.16	ALOGPS
logP	-3.5	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	0.84	ChemAxon
Physiological Charge	-6	ChemAxon
Hydrogen Acceptor Count	19	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	388.86 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	129.57 m³·mol⁻¹	ChemAxon
Polarizability	49.15 Å³	ChemAxon
Number of Rings	3	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:

Not Available

KEGG Pathways:

Purine metabolism ec00230

EcoCyc Pathways:

ppGpp biosynthesis PPGPPMET-PWY

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0k92-8972876000-b79a72511106591f97e8	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
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_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
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_15) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0900044000-e96c10f40cd9e086d540	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0900020000-b82fa0d9a9f331aa2a4b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-1900000000-baf8b81708e533b98dcb	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0f89-0720009000-1a3224060ede9e590dff	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0zir-5930000000-c118ece248c4154dc94a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-056r-8920000000-f5ca09c09ff793adde1f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0f89-0800009000-68b50d13f2eddae6a6c8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0900024000-314bc9a6cccb1860cf1f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03dl-0119700000-dcc092fec3a339f107b3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-0000029000-ac04ea79006ac6cf4eda	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0gz9-3000296000-109358d1b6f4dd2f2603	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100010000-63c1e0912d39faa514e4	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:

Chaloner-Larsson, G., Yamazaki, H. (1976). "Synthesis of guanosine 5'-triphosphate,3'-diphosphate in a spo T strain of Escherichia coli." Can J Biochem 54:935-940. Pubmed: 793688
Chatterji, D., Ojha, A. K. (2001). "Revisiting the stringent response, ppGpp and starvation signaling." Curr Opin Microbiol 4:160-165. Pubmed: 11282471
Heinemeyer, E. A., Richter, D. (1978). "Characterization of the guanosine 5'-triphosphate 3'-diphosphate and guanosine 5'-diphosphate 3'-diphosphate degradation reaction catalyzed by a specific pyrophosphorylase from Escherichia coli." Biochemistry 17:5368-5372. Pubmed: 365225
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

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	16690
HMDB ID	HMDB0060480
Pubchem Compound ID	38166
Kegg ID	C04494
ChemSpider ID	34987
Wikipedia ID	Not Available
BioCyc ID	GDP-TP
EcoCyc ID	GDP-TP
Ligand Expo	0O2

Enzymes

Protein Details

1. Exopolyphosphatase

General function:: Involved in magnesium ion binding
Specific function:: Degradation of inorganic polyphosphates. Orthophosphate is released progressively from the ends of polyphosphate of circa 500 residues long, while chains of circa 15 residues compete poorly with polyphosphate as substrate
Gene Name:: ppx
Uniprot ID:: P0AFL6
Molecular weight:: 58136

Reactions

(Polyphosphate)(n) + H(2)O = (polyphosphate)(n-1) + phosphate.

Protein Details

2. GTP pyrophosphokinase

General function:: Involved in amino acid binding
Specific function:: In eubacteria ppGpp (guanosine 3'-diphosphate 5-' diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance. This enzyme catalyzes the formation of pppGpp which is then hydrolyzed to form ppGpp
Gene Name:: relA
Uniprot ID:: P0AG20
Molecular weight:: 83875

Reactions

ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate.

Protein Details

3. Bifunctional (p)ppGpp synthase/hydrolase SpoT

General function:: Involved in catalytic activity
Specific function:: In eubacteria ppGpp (guanosine 3'-diphosphate 5-' diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance. This enzyme catalyzes both the synthesis and degradation of ppGpp. The second messengers ppGpp and c-di-GMP together control biofilm formation in response to translational stress; ppGpp represses biofilm formation while c- di-GMP induces it
Gene Name:: spoT
Uniprot ID:: P0AG24
Molecular weight:: 79342

Reactions

ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate.
Guanosine 3',5'-bis(diphosphate) + H(2)O = guanosine 5'-diphosphate + diphosphate.

Protein Details

4. Guanosine-5'-triphosphate,3'-diphosphate pyrophosphatase

General function:: Involved in guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity
Specific function:: Conversion of pppGpp to ppGpp. Guanosine pentaphosphate (pppGpp) is a cytoplasmic signaling molecule which together with ppGpp controls the "stringent response", an adaptive process that allows bacteria to respond to amino acid starvation, resulting in the coordinated regulation of numerous cellular activities
Gene Name:: gppA
Uniprot ID:: P25552
Molecular weight:: 54871

Reactions

Guanosine 5'-triphosphate,3'-diphosphate + H(2)O = guanosine 3',5'-bis(diphosphate) + phosphate.

Guanosine 3'-diphosphate 5'-triphosphate (ECMDB20156) (M2MDB001003)

Structure for #<Compound:0xa527fb78>

Enzymes

Reactions

Reactions

Reactions

Reactions