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Information on EC 2.5.1.16 - spermidine synthase and Organism(s) Escherichia coli and UniProt Accession P09158
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EC Tree
2.5.1.16 spermidine synthaseIUBMB Comments
The enzymes from the plant Glycine max and from mammalia are highly specific for putrescine as the amine acceptor [2,7]. The enzymes from the bacteria Escherichia coli and Thermotoga maritima prefer putrescine but are more tolerant towards other amine acceptors, such as spermidine and cadaverine [5,6]. cf. EC 2.5.1.22 (spermine synthase) and EC 2.5.1.23 (sym-norspermidine synthase).
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Word Map
- 2.5.1.16
- polyamine
- spermine
- s-adenosylmethionine
- ornithine
- diamine
- samdc
- dicyclohexylamine
- alpha-difluoromethylornithine
- 5'-methylthioadenosine
- cadaverine
- trypanothione
- adometdc
- agmatine
-
4.1.1.50
- difluoromethylornithine
- medicine
- drug development
- methylthioadenosine
- thermospermine
- nutrition
- 1,3-diaminopropane
- biotechnology
- norspermidine
-
multisubstrate
The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
Synonyms
spermidine synthase, aminopropyltransferase, spds2, spdsyn, spd synthase, mdspds1, spermidine synthase 1, pgspd, putrescine aminopropyltransferase, spermidine synthetase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
aminopropyltransferase
-
-
-
-
aminopropyltransferase spermidine synthase
-
-
-
-
putrescine aminopropyltransferase
-
-
-
-
spermidine synthetase
-
-
-
-
synthase, spermidine
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
S-adenosyl 3-(methylsulfanyl)propylamine + putrescine = S-methyl-5'-thioadenosine + spermidine
Escherichia coli SPDS follows the ping-pong mechanism, in which an aminopropylated enzyme intermediate was formed by the interaction of SPDS with dcSAM, prior to reaction with putrescine
S-adenosyl 3-(methylsulfanyl)propylamine + putrescine = S-methyl-5'-thioadenosine + spermidine
S-adenosyl 3-(methylsulfanyl)propylamine + putrescine = S-methyl-5'-thioadenosine + spermidine
first discovered
-
S-adenosyl 3-(methylsulfanyl)propylamine + putrescine = S-methyl-5'-thioadenosine + spermidine
ping-pong mechanism with a propylaminated form of the enzyme as an obligatory intermediate
-
S-adenosyl 3-(methylsulfanyl)propylamine + putrescine = S-methyl-5'-thioadenosine + spermidine
single displacement reaction
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
aminopropyl group transfer
-
-
-
-
PATHWAY SOURCE
PATHWAYS
BRENDA
-
-
SYSTEMATIC NAME
IUBMB Comments
S-adenosyl 3-(methylthio)propylamine:putrescine 3-aminopropyltransferase
The enzymes from the plant Glycine max and from mammalia are highly specific for putrescine as the amine acceptor [2,7]. The enzymes from the bacteria Escherichia coli and Thermotoga maritima prefer putrescine but are more tolerant towards other amine acceptors, such as spermidine and cadaverine [5,6]. cf. EC 2.5.1.22 (spermine synthase) and EC 2.5.1.23 (sym-norspermidine synthase).
CAS REGISTRY NUMBER
COMMENTARY
37277-82-0
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosylmethioninamine + putrescine
S-methyl-5'-thioadenosine + spermidine
-
-
-
?
S-adenosyl-(5')-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
S-adenosyl-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
S-adenosyl-3-methylthio-1-propylamine + 1,5-diaminopentane
5'-methylthioadenosine + N-(3-aminopropyl)-1,5-diaminopentane
S-adenosylmethioninamine + putrescine
5'-S-methyl-5'-thioadenosine + spermidine
-
-
-
-
?
S-adenosyl-(5')-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
-
-
-
?
S-adenosyl-(5')-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
-
-
-
?
S-adenosyl-(5')-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
-
-
-
?
S-adenosyl-(5')-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
-
-
-
?
S-adenosyl-(5')-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
-
-
-
?
S-adenosyl-(5')-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
-
-
-
?
S-adenosyl-(5')-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
-
-
-
ir
S-adenosyl-(5')-3-methylthio-1-propylamine + spermidine
5'-methylthioadenosine + spermine
-
at a reduced rate
-
-
?
S-adenosyl-(5')-3-methylthio-1-propylamine + spermidine
5'-methylthioadenosine + spermine
-
at a reduced rate
the reaction rate is slower than with 1,4-diaminobutane
?
S-adenosyl-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
-
-
-
?
S-adenosyl-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
-
-
-
?
S-adenosyl-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
-
-
-
?
S-adenosyl-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
-
-
-
?
S-adenosyl-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
-
-
-
?
S-adenosyl-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
-
-
-
?
S-adenosyl-3-methylthio-1-propylamine + 1,5-diaminopentane
5'-methylthioadenosine + N-(3-aminopropyl)-1,5-diaminopentane
-
-
-
?
S-adenosyl-3-methylthio-1-propylamine + 1,5-diaminopentane
5'-methylthioadenosine + N-(3-aminopropyl)-1,5-diaminopentane
-
-
-
-
?
S-adenosyl-3-methylthio-1-propylamine + 1,5-diaminopentane
5'-methylthioadenosine + N-(3-aminopropyl)-1,5-diaminopentane
-
-
aminopropylcadaverine
?
S-adenosyl-3-methylthio-1-propylamine + 1,5-diaminopentane
5'-methylthioadenosine + N-(3-aminopropyl)-1,5-diaminopentane
-
cadaverine
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosylmethioninamine + putrescine
S-methyl-5'-thioadenosine + spermidine
-
-
-
?
S-adenosyl-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
S-adenosyl-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
-
-
-
?
S-adenosyl-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
-
-
-
?
S-adenosyl-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
-
-
-
?
S-adenosyl-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
-
-
-
?
S-adenosyl-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
-
-
-
?
S-adenosyl-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Cyclohexylamine
-
potent inhibition, reduces the rate of spermidine synthesis by more than 90% at 0.1 mM
deaminated analogs of decarboxy-S-adenosyl-(5')-3-methylthiopropylamine
-
competitive inhibition with 1,4-diaminobutane and non-competitive with decarboxy-S-adenosyl-(5')-3-methylthiopropylamine
S-adenosyl-(5')-3-methylthio-1-propylamine
-
competitive substrate inhibition
S-Adenosyl-1,8-diamino-3-thiooctane
-
competitive with 1,4-diaminobutane, potent inhibition, stronger than dicyclohexylamine in vitro, but not in vivo, at concentrations of S-adenosyl-3-methylthio-1-propylamine and 1,4-diaminobutane higher than those normally present in vivo. At concentration of substrates that approximate in vivo conditions, more than 20fold stronger inhibition
S-Inosyl(5')-3-methylthiopropylamine
-
not S-inosyl(5')-3-methylthiopropanol
additional information
-
no inhibition by phenylhydrazine, semicarbazide, sodium borohydride, NaCN, KCl, NH4Cl, MgCl2, CaCl2, NaNO3, Na2SO4, Na2HPO4
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.029
S-adenosylmethioninamine
pH 7.5, 37°C, recombinant SPS mutant I163A
0.032
S-adenosylmethioninamine
pH 7.5, 37°C, recombinant wild-type enzyme
0.033
S-adenosylmethioninamine
pH 7.5, 37°C, recombinant SPS mutant C159S
0.035
S-adenosylmethioninamine
pH 7.5, 37°C, recombinant SPS mutant P162A
0.038
S-adenosylmethioninamine
pH 7.5, 37°C, recombinant SPS mutant C159A
0.05
S-adenosylmethioninamine
pH 7.5, 37°C, recombinant SPS mutant T160A
0.059
S-adenosylmethioninamine
pH 7.5, 37°C, recombinant SPS mutant P165A
0.0022
S-adenosyl-3-methylthio-1-propylamine
-
pH 8.0, 37ºC, fluorometric assay
0.0022
S-adenosyl-3-methylthio-1-propylamine
-
pH 8.2, 37ºC, spectrophotometric assay
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.128
S-adenosylmethioninamine
pH 7.5, 37°C, recombinant SPS mutant C159A
0.135
S-adenosylmethioninamine
pH 7.5, 37°C, recombinant SPS mutant T160A
0.138
S-adenosylmethioninamine
pH 7.5, 37°C, recombinant SPS mutant I163A
0.14
S-adenosylmethioninamine
pH 7.5, 37°C, recombinant wild-type enzyme
0.145
S-adenosylmethioninamine
pH 7.5, 37°C, recombinant SPS mutant C159S
0.15
S-adenosylmethioninamine
pH 7.5, 37°C, recombinant SPS mutant P165A
0.156
S-adenosylmethioninamine
pH 7.5, 37°C, recombinant SPS mutant P162A
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2.5
S-adenosylmethioninamine
pH 7.5, 37°C, recombinant SPS mutant P165A
2.7
S-adenosylmethioninamine
pH 7.5, 37°C, recombinant SPS mutant T160A
3.4
S-adenosylmethioninamine
pH 7.5, 37°C, recombinant SPS mutant C159A
4.4
S-adenosylmethioninamine
pH 7.5, 37°C, recombinant wild-type enzyme and SPS mutant C159S
4.5
S-adenosylmethioninamine
pH 7.5, 37°C, recombinant SPS mutant P162A
4.8
S-adenosylmethioninamine
pH 7.5, 37°C, recombinant SPS mutant I163A
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
10.4
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
8.6 - 10.6
-
about 65% of maximal activity at pH 8.6 and about 90% of maximal activity at pH 10.6
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37 - 50
sharp drop in activity above optimal temperature 50°C, profile overview
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
spermidine synthase plays a crucial role in cell proliferation and differentiation
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
33252
2 * 36500, 2 * 33823, recombinant His6-tagged enzyme, mass spectrometry, 2 * 33252, His6-tagged enzyme, sequence calculation
33823
2 * 36500, 2 * 33823, recombinant His6-tagged enzyme, mass spectrometry, 2 * 33252, His6-tagged enzyme, sequence calculation
36500
2 * 36500, 2 * 33823, recombinant His6-tagged enzyme, mass spectrometry, 2 * 33252, His6-tagged enzyme, sequence calculation
73000
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homodimer
2 * 36500, 2 * 33823, recombinant His6-tagged enzyme, mass spectrometry, 2 * 33252, His6-tagged enzyme, sequence calculation
dimer
dimer
-
2 * 37000-38000, high speed sedimentation equilibrium centrifugation in 6 M guanidine-HCl and 0.1 M 2-mercaptoethanol
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
using the hanging-drop vapour diffusion method. SpeE crystals diffract up to 2.9 A resolution using the Quantum 4-CCD detector. SpeE consists of two domains a small N-terminal beta-strand domain, and a C-terminal catalytic domain that adopts a canonical methyltransferase (MTase) Rossmann fold. Structural comparison of Escherichia coli SpeE to its homologs reveals that it has a large and unique substrate-binding cleft that may account for its lower amine substrate specificity
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C159A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
I163A
site-directed mutagenesis, replacement of Ile163 has no influence on EcSDPS activity
P162A
site-directed mutagenesis, replacement of Pro162 has no influence on EcSDPS activity
P165Q
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
T160A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
50
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, partially purified enzyme, several weeks with less than 20% loss of activity
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain SG13009
extraction, ammonium sulfate fractionation, chromatography on calcium phosphate cellulose, DEAE-Sephadex, chromatography on hydroxyapatite, disc gel electrophoresis
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant overexpression of His6-tagged wild-type and mutant enzymes in Escherichia coli strain SG13009
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Tabor, H.; Tabor, C.W.
Biosynthesis and metabolism of 1,4-diaminobutane, spermidine, spermine, and related amines
Adv. Enzymol. Relat. Areas Mol. Biol.
36
203-268
1972
Saccharomyces cerevisiae, Escherichia coli, Neurospora crassa, Rattus norvegicus
Pegg, A.E.; Bitonti, A.J.; McCann, P.P.; Coward, J.K.
Inhibition of bacterial aminopropyltransferases by S-adenosyl-1,8-diamino-3-thiooctane and by dicyclohexylamine
FEBS Lett.
155
192-196
1983
Escherichia coli, Pseudomonas aeruginosa, Rattus norvegicus, Serratia marcescens
Sindhu, R.K.; Cohen, S.S.
Putrescine aminopropyltransferase (spermidine synthase) of Chinese Cabbage
Methods Enzymol.
94
279-285
1983
Brassica rapa subsp. pekinensis, Escherichia coli
-
Bowman, W.H.; White Tabor, C.; Tabor, H.
Spermidine biosynthesis. Purification and properties of propylamine transferase from Escherichia coli
J. Biol. Chem.
248
2480-2486
1973
Escherichia coli
White Tabor, C.; Tabor, H.
Putrescine aminopropyltransferase (Escherichia coli)
Methods Enzymol.
94
265-270
1983
Escherichia coli
Zappia, V.; Cacciapuoti, G.; Pontoni, G.; Oliva, A.
Mechanism of propylamine-transfer reactions. Kinetic and inhibition studies on spermidine synthase from Escherichia coli
J. Biol. Chem.
255
7276-7280
1980
Escherichia coli
Samejima, K.; Yamanoha, B.
Purification of spermidine synthase from rat ventral prostate by affinity chromatography on immobilized S-adenosyl(5)-3-thiopropylamine
Arch. Biochem. Biophys.
216
213-222
1982
Escherichia coli, Rattus norvegicus, Rattus norvegicus Wistar
Zhou, X.; Chua, T.K.; Tkaczuk, K.L.; Bujnicki, J.M.; Sivaraman, J.
The crystal structure of Escherichia coli spermidine synthase SpeE reveals a unique substrate-binding pocket
J. Struct. Biol.
169
277-285
2010
Escherichia coli
EXTERNAL LINKS (specific for EC-Number 2.5.1.16)
Transporter Classification Database (TCDB): 2.A.1.86.5
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