Ligand spermidine

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Basic Ligand Information

Molecular Structure

C₇H₁₉N₃

spermidine

ATHGHQPFGPMSJY-UHFFFAOYSA-N

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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, spermidine[side 2]

Related pathways

BRENDA

alanine metabolism, glutathione metabolism, polyamine pathway

KEGG

ABC transporters, Arginine and proline metabolism, beta-Alanine metabolism, Bile secretion, Biosynthesis of siderophore group nonribosomal peptides

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MetaCyc

beta-alanine biosynthesis IV, branched-chain polyamines biosynthesis, glutathionylspermidine biosynthesis, homospermidine biosynthesis I, hypusine biosynthesis

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Show all BRENDA pathways known for spermidine

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Roles as Enzyme Ligand

In Vivo Substrate in Enzyme-catalyzed Reactions (46 results)

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1.4.3.21

spermidine + H2O + O2 = ?

spermidine + O2 + H2O = putrescine + 3-aminobutanal + H2O2

spermidine + cytochrome c = 1,3-diaminopropane + gamma-aminobutylaldehyde

392545, 392546

2.3.1.248

2 sinapoyl-CoA + spermidine = 2 CoA + N1,N8-bis(sinapoyl)-spermidine

S-adenosyl 3-(methylthio)propylamine + spermidine = S-methyl-5'-thioadenosine + thermospermine + H+

727512

2.5.1.127

S-adenosyl 3-(methylthio)propylamine + spermidine = S-methyl-5'-thioadenosine + thermospermine + H+

727512

2.5.1.128

2 S-adenosyl 3-(methylthio)propylamine + spermidine = 2 S-methyl-5'-thioadenosine + N4-bis(aminopropyl)spermidine

spermidine + 8-amino-7-oxononanoate = N-(3-aminopropyl)-4-aminobutanal + 7,8-diaminononanoate

In Vivo Product in Enzyme-catalyzed Reactions (48 results)

glutathionylspermidine + H2O = glutathione + spermidine

3.5.3.24

N1-aminopropylagmatine + H2O = spermidine + urea

4.1.1.96

carboxyspermidine = spermidine + CO2

7.6.2.11

ATP + H2O + spermidine-[polyamine-binding protein][side 1] = ADP + phosphate + spermidine[side 2] + [polyamine-binding protein][side 1]

8Y5G, 3D-view

7.6.2.16

ATP + H2O + spermidine-[spermidine-binding protein][side 1] = ADP + phosphate + spermidine[side 2] + [spermidine-binding protein][side 1]

Substrate in Enzyme-catalyzed Reactions (184 results)

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1.14.13.252

spermidine + NADPH + H+ + O2 = N-hydroxyspermidine + NADP+ + H2O

775346

1.4.3.10

spermidine + O2 + H2O = 4-aminobutyraldehyde + 1,3-diaminopropane + H2O2

395437, 395450, 395448, 395449, 395442, 395444, 395447, 288077, 684634, 725184, 724877

1.4.3.13

spermidine + O2 + H2O = ?

spermidine + 2 O2 + H2O = ?

767738

1.4.9.2

spermidine + H2O + 2,6-dichlorophenol indophenol = ? + NH3 + reduced 2,6-dichlorophenol indophenol

655062

1.5.3.13

spermidine + O2 + H2O = ?

carbamoyl phosphate + spermidine = phosphate + N-carbamoylspermidine

2 sinapoyl-CoA + spermidine = 2 CoA + N1,N8-bis(sinapoyl)-spermidine

acetyl-CoA + spermidine = CoA + ?

762682

2.3.1.48

acetyl-CoA + spermidine = ?

487064, 487060, 487074, 487062, 756126

S-adenosyl 3-(methylthio)propylamine + spermidine = S-methyl-5'-thioadenosine + thermospermine + H+

727512

2.5.1.127

S-adenosyl 3-(methylthio)propylamine + spermidine = S-methyl-5'-thioadenosine + thermospermine + H+

spermidine + 8-amino-7-oxononanoate = N-(3-aminopropyl)-4-aminobutanal + 7,8-diaminononanoate

778975

2.6.1.77

spermidine + pyruvate = ? + L-alanine

662781

2.6.1.82

spermidine + 2-oxoglutarate = ?

661399

3.5.1.B21

triglycine + spermidine = triglycylspermidine + H2O

Product in Enzyme-catalyzed Reactions (131 results)

spermine + O2 + H2O = spermidine + propane-1,3-diamine + H2O2

2 CoA + N1,N8-bis(sinapoyl)-spermidine = 2 sinapoyl-CoA + spermidine

6LPW, 3D-view

2.5.1.104

S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine

2.5.1.16

66 entries

2.5.1.23

S-adenosylmethioninamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine

2.5.1.44

putrescine + 1,3-diaminopropane = homospermidine + spermidine

spermidine-ubiquitin + H2O = ubiquitin + spermidine

9BLN, 3D-view

3.5.1.4

acetylspermidine + H2O = acetate + spermidine

glutathionylspermidine + H2O = glutathione + spermidine

967, 968, 969, 31903, 649733, -

3.5.3.24

N1-aminopropylagmatine + H2O = spermidine + urea

4.1.1.96

carboxyspermidine = spermidine + CO2

4.3.2.8

L-gamma-glutamylspermidine = spermidine + 5-oxo-L-proline

6.3.1.8

glutathionylspermidine + H2O = glutathione + spermidine

ATP + H2O + spermidine-[spermidine-binding protein][side 1] = ADP + phosphate + spermidine[side 2] + [spermidine-binding protein][side 1]

Activator in Enzyme-catalyzed Reactions (106 results)

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1.1.1.49

activation constant: 0.2 mM

722577

1.5.1.2

10% activation at 1.2 mM

1 mM, stimulation

up to 2.5 fold stimulation at 1 mm

441207

2.1.1.193

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

662755

2.4.1.207

1 mM, slighly activates

636810

2.4.1.94

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

645747

3.1.1.11

activates with increasing temperature to a maximal value at 45°C

0.8 mM, markedly stimulates hydrolysis of D-Tyr-tRNATyr

725371

3.1.13.1

can replace missing Mg2+ to a small extent

divalent cation, metal or polyamine is required, 0.3 mM is as effective as Mg2+

PLC d1

EC50: about 1 mM

stimulates activity

stimulates, maximal stimulation at 1 mM, inhibition above

647264

3.4.21.36

spermidine serves as a partial stabilizer and an activator for the enzyme

753855

3.4.21.53

activation, at physiological concentration, ATP hydrolysis and protease activity

slowly enhances activity between 5 mM and 25 mM

753847

3.5.3.12

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.

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

114

6.1.1.19

supports aminoacylation in presence of crude tRNA not in presence of resolved tRNA

5 mM, increases the Km for nicked DNA, increases reaction velocity

1929

Inhibitor in Enzyme-catalyzed Reactions (124 results)

80% residual activity at 0.05 mg

733523

1.14.99.29

58% of initial activity at 0.5 mM

438288

1.4.3.10

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

690217

2.1.1.35

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

662755

2.3.1.48

inhibits histone acetylation at high concentrations, enzyme forms A and B

487064

2.3.1.57

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

645326

3.1.14.1

slight inhibition: 80% of maximal activity with 0.01 M

134099

3.1.26.4

inhibition of Mn2+-dependent enzyme, no inhibition of the Mg2+-dependent enzyme

inhibition above 1 mM

647264

3.4.21.64

effect of spermidine on the structure, kinetics and stability of proteinase K, analysis with respect to industrial and biological applications of the enzyme. Molecular docking study and simulations, molecular dynamics data analysis, overview

spermidine trihydrochloride acts as an inhibitor bonded to the pepsin-BSA-BPB complex. Induced changes by spermidine trihydrochloride in the conformation and dynamic properties of the pepsin active cause a decrease in the amounts of pepsin activity parameters (Km, Kcat, Km/Kcat, and Vmax) in the presence of the ligand and finally lead to pepsin inactivation. Fluorescence quenching mechanism of spermidine, molecular dynamic simulation, molecular docking, overview

over 80% inhibition at 1 mM

769476

3.5.3.1

inhibition in a dose-dependent fashion below 5 mM and above 25 mM

0.5 mg/ml, complete inhibition

0.17 mM, 50% loss of activity

2mM

4078, 4080, 4082, 4083, 4085, 4086, 4094, 4097, 4099, 4101

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

putrescine uptake by the enzyme is gradually inhibited by increasing levels of spermidine

752458

Metals and Ions (1 result)

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3.1.21.10

666746

3D Structure of Enzyme-Ligand-Complex (PDB) (718 results)

Enzyme Kinetic Parameters

k_cat Value (Turnover Number) (61 results)

0.1

pH 7.5, 25°C, recombinant AtPAO4

5.6

pH 7.3, 30°C, recombinant His6-tagged enzyme

734888

2.3.1.249

3.1

pH 7.3, 30°C, recombinant His6-tagged enzyme

0.65

pH 9.0, 37°C

4.2

pH 7.2, 25°C, recombinant trypanothione synthase performing the glutathionylspermidine synthase reaction

662446

6.3.1.9

28.6

971

K_M Value (151 results)

0.015

addition of 5 mM benzyldehyde, hPAO

19.7

0.0374

pH 7.3, 30°C, recombinant His6-tagged enzyme

734888

2.3.1.249

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

719387

2.5.1.44

1.5

in presence of 1 mM putrescine

288699, 288702

2.5.1.45

0.012

at 0.1 mM putrescine

0.104

0.059

pH 7.3, synthetase activity

0.001

spermidine-preferential system

657330

K_i Value (12 results)

0.181

0.19

0.546

pH 8.0, substrate: spermine

0.9

0.094

0.00649

0.00248

pH 2.0, 37Â°C

776023

3.5.1.48

0.31

172053

References & Links

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Show Reference (536 entries)

Links to other databases for spermidine

Ligand spermidine

Basic Ligand Information

Related pathways

Roles as Enzyme Ligand

In Vivo Substrate in Enzyme-catalyzed Reactions (46 results)

In Vivo Product in Enzyme-catalyzed Reactions (48 results)

Substrate in Enzyme-catalyzed Reactions (184 results)

Product in Enzyme-catalyzed Reactions (131 results)

Activator in Enzyme-catalyzed Reactions (106 results)

Inhibitor in Enzyme-catalyzed Reactions (124 results)

Metals and Ions (1 result)

3D Structure of Enzyme-Ligand-Complex (PDB) (718 results)

Enzyme Kinetic Parameters

kcat Value (Turnover Number) (61 results)

KM Value (151 results)

Ki Value (12 results)

References & Links

Literature References (536)

Links to other databases for spermidine

k_cat Value (Turnover Number) (61 results)

K_M Value (151 results)

K_i Value (12 results)