Ligand spermidine

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Basic Ligand Information

Molecular Structure
Picture of spermidine (click for magnification)
Molecular Formula
BRENDA Name
InChIKey
C7H19N3
spermidine
ATHGHQPFGPMSJY-UHFFFAOYSA-N
Synonyms:
H2N(CH2)3NH(CH2)4NH2, N(3-aminopropyl)butane-1,4-diamine, N-(3-aminopropy)1,4-butanediamine, N-(3-aminopropyl)-1,4-butane-diamine, N-(3-aminopropyl)butane-1,4-diamine, N-(gamma-aminopropyl)tetramethylenediamine, spermidine-HCl


Show all pahtways known for Show all BRENDA pathways known for spermidine

Roles as Enzyme Ligand

In Vivo Substrate in Enzyme-catalyzed Reactions (30 results)

EC NUMBER
PROVEN IN VIVO REACTION
REACTION DIAGRAM
LITERATURE
ENZYME 3D STRUCTURE
spermidine + H2O + O2 = ?
show the reaction diagram
-
spermidine + cytochrome c = 1,3-diaminopropane + gamma-aminobutylaldehyde
show the reaction diagram
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2 sinapoyl-CoA + spermidine = 2 CoA + N1,N8-bis(sinapoyl)-spermidine
show the reaction diagram
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2 4-coumaroyl-CoA + spermidine = 2 CoA + N1,N8-bis(4-coumaroyl)-spermidine
show the reaction diagram
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S-adenosyl 3-(methylthio)propylamine + spermidine = S-methyl-5'-thioadenosine + thermospermine + H+
show the reaction diagram
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S-adenosyl 3-(methylthio)propylamine + spermidine = S-methyl-5'-thioadenosine + thermospermine + H+
show the reaction diagram
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2 S-adenosyl 3-(methylthio)propylamine + spermidine = 2 S-methyl-5'-thioadenosine + N4-bis(aminopropyl)spermidine
show the reaction diagram
putrescine + spermidine = sym-homospermidine + propane-1,3-diamine
show the reaction diagram
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In Vivo Product in Enzyme-catalyzed Reactions (25 results)

EC NUMBER
PROVEN IN VIVO REACTION
REACTION DIAGRAM
LITERATURE
ENZYME 3D STRUCTURE
spermine + O2 + H2O = spermidine + 3-aminopropanal + H2O2
show the reaction diagram
-
-
N1-acetylspermidine + H2O = acetate + spermidine
show the reaction diagram
-
-
glutathionylspermidine + H2O = glutathione + spermidine
show the reaction diagram
-
-
N1-aminopropylagmatine + H2O = spermidine + urea
show the reaction diagram
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-

Substrate in Enzyme-catalyzed Reactions (109 results)

EC NUMBER
REACTION
REACTION DIAGRAM
LITERATURE
ENZYME 3D STRUCTURE
spermidine + O2 + H2O = ?
show the reaction diagram
-
spermidine + H2O + 2,6-dichlorophenol indophenol = ? + NH3 + reduced 2,6-dichlorophenol indophenol
show the reaction diagram
-
spermidine + O2 + H2O = ?
show the reaction diagram
-
carbamoyl phosphate + spermidine = phosphate + N-carbamoylspermidine
show the reaction diagram
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2 sinapoyl-CoA + spermidine = 2 CoA + N1,N8-bis(sinapoyl)-spermidine
show the reaction diagram
-
2 4-coumaroyl-CoA + spermidine = 2 CoA + N1,N8-bis(4-coumaroyl)-spermidine
show the reaction diagram
-
acetyl-CoA + spermidine = ?
show the reaction diagram
-
S-adenosyl 3-(methylthio)propylamine + spermidine = S-methyl-5'-thioadenosine + thermospermine + H+
show the reaction diagram
-
S-adenosyl 3-(methylthio)propylamine + spermidine = S-methyl-5'-thioadenosine + thermospermine + H+
show the reaction diagram
-
spermidine + pyruvate = ? + L-alanine
show the reaction diagram
-
spermidine + 2-oxoglutarate = ?
show the reaction diagram
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Product in Enzyme-catalyzed Reactions (86 results)

EC NUMBER
REACTION
REACTION DIAGRAM
LITERATURE
ENZYME 3D STRUCTURE
spermine + O2 + H2O = spermidine + propane-1,3-diamine + H2O2
show the reaction diagram
-
2 CoA + N1,N8-bis(sinapoyl)-spermidine = 2 sinapoyl-CoA + spermidine
show the reaction diagram
-
-
S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine
show the reaction diagram
-
-
S-adenosylmethioninamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine
show the reaction diagram
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-
putrescine + 1,3-diaminopropane = homospermidine + spermidine
show the reaction diagram
-
caldine + putrescine = spermidine + ?
show the reaction diagram
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spermidine-ubiquitin + H2O = ubiquitin + spermidine
show the reaction diagram
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-
acetylspermidine + H2O = acetate + spermidine
show the reaction diagram
-
-
N8-acetylspermidine + H2O = acetate + spermidine
show the reaction diagram
-
-
glutathionylspermidine + H2O = glutathione + spermidine
show the reaction diagram
-
N1-aminopropylagmatine + H2O = spermidine + urea
show the reaction diagram
-
-
carboxyspermidine = spermidine + CO2
show the reaction diagram
-
-
L-gamma-glutamylspermidine = spermidine + 5-oxo-L-proline
show the reaction diagram
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-
glutathionylspermidine + H2O = glutathione + spermidine
show the reaction diagram
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Activator in Enzyme-catalyzed Reactions (87 results)

EC NUMBER
COMMENTARY
LITERATURE
ENZYME 3D STRUCTURE
activation constant: 0.2 mM
-
10% activation at 1.2 mM
-
1 mM, stimulation
enzyme optimally activated by phospholipids is additionally activated 2fold
-
up to 2.5 fold stimulation at 1 mm
-
in the presence of spermidine, Mg2+ is not required for activity. Activity could be restored up to 60% of that with Mg2+ by addition of spermidine at 30 mM
-
activates at 5 mM
-
activates about 3.5fold in presence of 0.1 mg/ml bovine serum albumin
-
1 mM, slighly activates
-
most effective activator, 10-15 mM
-
increases activity
-
stimulates
-
half-maximal stimulation at 1.5 mM
-
enhances activity
-
aliphatic, positively charged polyamine, required for in vitro activity of ORF47, polyamine depletion leads to 80% reduced activity
-
slight stimulation
-
slight stimulation, 5 mM
-
stimulates, optimum concentration: 4.0 mM
-
activates with increasing temperature to a maximal value at 45°C
-
0.8 mM, markedly stimulates hydrolysis of D-Tyr-tRNATyr
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can replace missing Mg2+ to a small extent
-
divalent cation, metal or polyamine is required, 0.3 mM is as effective as Mg2+
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PLC d1
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EC50: about 1 mM
-
stimulates activity
-
stimulates, maximal stimulation at 1 mM, inhibition above
-
activation, at physiological concentration, ATP hydrolysis and protease activity
-
at concentration of 0.1 g/l about 10% more putrescine production, at concentration of 1 g/l 32% more putrescine production
-
ADC is analyzed in plants treated with spermidine and compared with untreated plants and with positive (TMV-inoculated or DL-beta-aminobutyric acid-treated) controls. ADC transcripts are significantly increased, at both the local and systemic levels, relative to untreated controls.
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enhances activity against poly(C) and yeast RNA, reverses inhibition by poly(G) by removal of inhibitor from the enzymes surface
-
can partially replace Mg2+ in activation, with 12% efficiency
-
supports aminoacylation in presence of crude tRNA not in presence of resolved tRNA
-
5 mM, increases the Km for nicked DNA, increases reaction velocity
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Inhibitor in Enzyme-catalyzed Reactions (100 results)

EC NUMBER
COMMENTARY
LITERATURE
ENZYME 3D STRUCTURE
80% residual activity at 0.05 mg
-
58% of initial activity at 0.5 mM
-
competitive inhibition of putrescine oxidation
-
substrate inhibition
-
12 mM
-
the early decrease of glutathione reductase activity in leaves treated with polyamines can be due to a direct interaction of these compounds with the enzyme
-
inhibition at optimal Mg2+-concentration
-
1 mM, 78% inhibition in the presence of 0.5 mM N-acetyl-L-glutamate
-
inhibits slightly in absence of bovine serum albumin
-
inhibits histone acetylation at high concentrations, enzyme forms A and B
-
0.005 mM, strong inhibition of eIF5A acetylation
competitive to L-arginyl-tRNA
-
competitive
-
15-34% inhibition with 5 mM; 15-34% inhibition with 5 mM; 15-34% inhibition with 5 mM
-
weak
-
potent inhibitor
-
weak, less potent than polylysine
-
3 mM
-
78% of maximal activity
-
slight inhibition: 80% of maximal activity with 0.01 M
-
inhibition of Mn2+-dependent enzyme, no inhibition of the Mg2+-dependent enzyme
-
inhibition above 1 mM
-
0.5 mg/ml, complete inhibition
-
0.17 mM, 50% loss of activity
-
2mM
-
RNA-binding enzyme activity is regulated through spermidine-induced changes in the charge and structure of the RNA substrate. Spermidine transiently stabilizes RNA sub-populations by binding both specifically and nonspecifically
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Metals and Ions (1 result)

EC NUMBER
COMMENTARY
LITERATURE
ENZYME 3D STRUCTURE

3D Structure of Enzyme-Ligand-Complex (PDB) (19 results)

Enzyme Kinetic Parameters

kcat Value (Turnover Number) (46 results)

EC NUMBER
TURNOVER NUMBER [1/S]
TURNOVER NUMBER MAXIMUM [1/S]
COMMENTARY
LITERATURE
5.6
-
pH 7.3, 30°C, recombinant His6-tagged enzyme
3.1
-
pH 7.3, 30°C, recombinant His6-tagged enzyme
0.65
-
pH 9.0, 37°C
0.015
-
pH 7.5, 37°C, heterotetrameric DHS; pH 7.5, 37°C, heterotetrameric DHS
4.2
-
pH 7.2, 25°C, recombinant trypanothione synthase performing the glutathionylspermidine synthase reaction
28.6
-
-

KM Value (137 results)

EC NUMBER
KM VALUE [MM]
KM VALUE MAXIMUM [MM]
COMMENTARY
LITERATURE
0.015
-
addition of 5 mM benzyldehyde, hPAO
19.7
-
-
0.0374
-
pH 7.3, 30°C, recombinant His6-tagged enzyme
0.0527
-
pH 7.3, 30°C, recombinant His6-tagged enzyme
0.00173
-
pH 9.0, 37°C
1.539
-
pH 7.5, 78°C
0.012
-
at 0.1 mM putrescine
0.104
-
-
0.059
-
pH 7.3, synthetase activity
0.001
-
spermidine-preferential system

Ki Value (10 results)

EC NUMBER
KI VALUE [MM]
KI VALUE MAXIMUM [MM]
COMMENTARY
LITERATURE
0.181
-
-
0.19
-
-
0.546
-
pH 8.0, substrate: spermine
0.9
-
-
0.094
-
-
0.00649
-
-
2
5
pH 8.0, 37°C
0.31
-
-

References & Links

Links to other databases for spermidine

ChEBI
PubChem
ChEBI
PubChem