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Escherichia coli K-12 substr. MG1655 Compound: GDP

Synonyms: ppG, guanosine-5'-diphosphate, guanosine-diphosphate

Superclasses: a nucleic acid component a nucleotide a nucleoside diphosphate a ribonucleoside diphosphate a purine ribonucleoside 5'-diphosphate
a nucleic acid component a nucleotide a purine nucleotide a purine ribonucleotide a purine ribonucleoside 5'-diphosphate
a nucleic acid component a nucleotide a ribonucleotide a purine ribonucleotide a purine ribonucleoside 5'-diphosphate
a nucleic acid component a nucleotide a ribonucleotide a ribonucleoside diphosphate a purine ribonucleoside 5'-diphosphate
a nucleic acid component
an organic heterocyclic compound an organic heterobicyclic compound a purine a purine nucleotide a purine ribonucleotide a purine ribonucleoside 5'-diphosphate
an organic heterocyclic compound an organonitrogen heterocyclic compound a purine a purine nucleotide a purine ribonucleotide a purine ribonucleoside 5'-diphosphate

Chemical Formula: C10H12N5O11P2

Molecular Weight: 440.18 Daltons

Monoisotopic Molecular Weight: 443.0243293706 Daltons

GDP compound structure

SMILES: C(OP(=O)([O-])OP(=O)([O-])[O-])C1(OC(C(O)C(O)1)N3(C=NC2(C(=O)NC(N)=NC=23)))

InChI: InChI=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)/p-3/t3-,5-,6-,9-/m1/s1

InChIKey: InChIKey=QGWNDRXFNXRZMB-UUOKFMHZSA-K

Unification Links: CAS:146-91-8 , ChEBI:58189 , ChemSpider:10239187 , HMDB:HMDB01201 , IAF1260:33599 , KEGG:C00035 , MetaboLights:MTBLC58189 , PubChem:21604868

Standard Gibbs Free Energy of Change Formation (ΔfG in kcal/mol): -559.979

Reactions known to consume the compound:

guanosine deoxyribonucleotides de novo biosynthesis II :
dGDP + an oxidized thioredoxin + H2O ← GDP + a reduced thioredoxin
dGDP + an oxidized NrdH glutaredoxin-like protein + H2O ← GDP + a reduced NrdH glutaredoxin-like protein

guanosine ribonucleotides de novo biosynthesis :
GDP + ATP → GTP + ADP

ppGpp biosynthesis :
GDP + ATP → GTP + ADP
ATP + GDP → AMP + ppGpp

Not in pathways:
GDP + H2O → GMP + phosphate + H+

Not in pathways:
an oxidized thioredoxin + a 2'-deoxyribonucleoside 5'-diphosphate + H2O ← a reduced thioredoxin + a ribonucleoside diphosphate

Not in pathways:
a nucleoside diphosphate + H2O → a nucleoside 5'-monophosphate + phosphate + H+
a nucleoside diphosphate + ATP → a nucleoside triphosphate + ADP

Reactions known to produce the compound:

adenosine ribonucleotides de novo biosynthesis :
L-aspartate + IMP + GTP → adenylo-succinate + GDP + phosphate + 2 H+

guanosine ribonucleotides de novo biosynthesis :
GMP + ATP → GDP + ADP

ppGpp biosynthesis :
ppGpp + H2O → GDP + diphosphate + H+

salvage pathways of pyrimidine ribonucleotides :
cytidine + GTP → CMP + GDP + H+
uridine + GTP → UMP + GDP + H+

Not in pathways:
GDP-α-D-mannose + H2O → D-mannose + GDP + H+
GDP-α-D-glucose + H2O → β-D-glucopyranose + GDP + H+
GTP + H2O → GDP + phosphate + H+
a 2-thiouridine34 in tRNA + a 5,10-methylene-tetrahydrofolate + ammonium + GTP + H2O → a 5-aminomethyl-2-thiouridine in tRNA + a 7,8-dihydrofolate + GDP + phosphate
GTP + AMP → GDP + ADP

tRNA processing :
a tRNA precursor with a 5' extension and a short 3' extension + n phosphate → a tRNA precursor with a 5' extension + a ribonucleoside diphosphate
a tRNA precursor with a short 3' extension + n phosphate → an uncharged tRNA + n a ribonucleoside diphosphate

Reactions known to both consume and produce the compound:

Not in pathways:
a single-stranded RNA + phosphate ↔ a single-stranded RNA + a nucleoside diphosphate

In Reactions of unknown directionality:

Not in pathways:
a uridine34 in tRNA + GTP + a 5,10-methylene-tetrahydrofolate + glycine + H2O = a 5-carboxymethylaminomethyluridine in tRNA + GDP + a 7,8-dihydrofolate + phosphate
a 2-thiouridine34 in tRNA + GTP + glycine + a 5,10-methylene-tetrahydrofolate + H2O = a 5-carboxymethylaminomethyl-2-thiouridine in tRNA + GDP + a 7,8-dihydrofolate + phosphate

Not in pathways:
RNA(n+1) + phosphate = RNA(n) + a nucleoside diphosphate

Enzymes activated by GDP, sorted by the type of activation, are:

Activator (Allosteric) of: thymidine kinase [Iwatsuki67, Chen78a] , 6-phosphofructokinase [Blangy68]

Activator (Mechanism unknown) of: ornithine decarboxylase [Kanjee11a] , amidophosphoribosyl transferase [Messenger79]

Enzymes inhibited by GDP, sorted by the type of inhibition, are:

Inhibitor (Competitive) of: GDP-mannose mannosyl hydrolase [Legler02] , GTP cyclohydrolase [Yim76] , nucleoside diphosphate kinase [Roisin78, Comment 1] , guanylate kinase [Oeschger66, Comment 2] , GDP-fucose synthase [Menon99]

Inhibitor (Noncompetitive) of: guanosine kinase [Kawasaki00, Comment 3]

Inhibitor (Mechanism unknown) of: guanosine kinase [Kawasaki00] , deoxyguanosine triphosphate triphosphohydrolase [Kornberg58]

This compound has been characterized as an alternative substrate of the following enzymes: polyphosphate kinase , pyruvate kinase , ATP synthase , pyruvate kinase


References

Blangy68: Blangy D, Buc H, Monod J (1968). "Kinetics of the allosteric interactions of phosphofructokinase from Escherichia coli." J Mol Biol 31(1);13-35. PMID: 4229913

Chen78a: Chen MS, Prusoff WH (1978). "Thymidine kinase from Escherichia coli." Methods Enzymol 1978;51;354-60. PMID: 357898

Iwatsuki67: Iwatsuki N, Okazaki R (1967). "Mechanism of regulation of deoxythymidine kinase of Escherichia coli. I. Effect of regulatory deoxynucleotides on the state of aggregation of the enzyme." J Mol Biol 1967;29(1);139-54. PMID: 4861610

Kanjee11a: Kanjee U, Gutsche I, Ramachandran S, Houry WA (2011). "The Enzymatic Activities of the Escherichia coli Basic Aliphatic Amino Acid Decarboxylases Exhibit a pH Zone of Inhibition." Biochemistry 50(43);9388-98. PMID: 21957966

Kawasaki00: Kawasaki H, Shimaoka M, Usuda Y, Utagawa T (2000). "End-product regulation and kinetic mechanism of guanosine-inosine kinase from Escherichia coli." Biosci Biotechnol Biochem 2000;64(5);972-9. PMID: 10879466

Kornberg58: Kornberg SR, Lehman IR, Bessman MJ, Simms ES, Kornberg A (1958). "Enzymatic cleavage of deoxyguanosine triphosphate to deoxyguanosine and tripolyphosphate." J Biol Chem 1958; 233:159-162. PMID: 13563461

Legler02: Legler PM, Lee HC, Peisach J, Mildvan AS (2002). "Kinetic and magnetic resonance studies of the role of metal ions in the mechanism of Escherichia coli GDP-mannose mannosyl hydrolase, an unusual nudix enzyme." Biochemistry 41(14);4655-68. PMID: 11926828

Menon99: Menon S, Stahl M, Kumar R, Xu GY, Sullivan F (1999). "Stereochemical course and steady state mechanism of the reaction catalyzed by the GDP-fucose synthetase from Escherichia coli." J Biol Chem 274(38);26743-50. PMID: 10480878

Messenger79: Messenger LJ, Zalkin H (1979). "Glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli. Purification and properties." J Biol Chem 1979;254(9);3382-92. PMID: 372191

Oeschger66: Oeschger MP, Bessman MJ (1966). "Purification and properties of guanylate kinase from Escherichia coli." J Biol Chem 1966;241(22);5452-60. PMID: 5333666

Roisin78: Roisin MP, Kepes A (1978). "Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme." Biochim Biophys Acta 1978;526(2);418-28. PMID: 214126

Yim76: Yim JJ, Brown GM (1976). "Characteristics of guanosine triphosphate cyclohydrolase I purified from Escherichia coli." J Biol Chem 1976;251(16);5087-94. PMID: 821948


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Wed Jul 29, 2015, biocyc12.