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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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IUBMB 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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This record set is specific for:
Escherichia coli
UNIPROT: P09158
Word Map
The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
Synonyms
spermidine synthase, aminopropyltransferase, spds2, spdsyn, spd synthase, mdspds1, putrescine aminopropyltransferase, spermidine synthase 1, pgspd, spermidine synthetase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
aminopropyltransferase
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-
-
0
aminopropyltransferase spermidine synthase
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-
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0
putrescine aminopropyltransferase
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-
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0
SPDS
298661
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spermidine synthase
246
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spermidine synthetase
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-
-
0
synthase, spermidine
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-
-
0
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
S-adenosyl 3-(methylsulfanyl)propylamine + putrescine = S-methyl-5'-thioadenosine + spermidine
show the reaction diagram
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
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
aminopropyl group transfer
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-
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0
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 hide
37277-82-0
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
S-adenosylmethioninamine + putrescine
S-methyl-5'-thioadenosine + spermidine
show the reaction diagram
-
-
-
?
S-adenosyl-(5')-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
show the reaction diagram
S-adenosyl-(5')-3-methylthio-1-propylamine + spermidine
5'-methylthioadenosine + spermine
show the reaction diagram
S-adenosyl-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
show the reaction diagram
S-adenosyl-3-methylthio-1-propylamine + 1,5-diaminopentane
5'-methylthioadenosine + N-(3-aminopropyl)-1,5-diaminopentane
show the reaction diagram
S-adenosylmethioninamine + putrescine
5'-S-methyl-5'-thioadenosine + spermidine
show the reaction diagram
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-
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
S-adenosylmethioninamine + putrescine
S-methyl-5'-thioadenosine + spermidine
show the reaction diagram
-
-
-
?
S-adenosyl-3-methylthio-1-propylamine + 1,4-diaminobutane
5'-methylthioadenosine + spermidine
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
-
no cofactor requirement
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
no metal ion requirement
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5'-ethylthioadenosine
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5'-methylthioadenosine
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W strain
Cyclohexylamine
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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
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competitive inhibition with 1,4-diaminobutane and non-competitive with decarboxy-S-adenosyl-(5')-3-methylthiopropylamine
N-ethylmaleimide
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p-hydroxymercuribenzoate
S-Adenosyl(5')-3-methylthiopropanol
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kinetics
S-adenosyl-(5')-3-methylthio-1-propylamine
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competitive substrate inhibition
S-Adenosyl-1,8-diamino-3-thiooctane
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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
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not S-inosyl(5')-3-methylthiopropanol
spermidine
sulfhydryl reagents
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W strain
additional information
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0778
putrescine
pH 7.5, 37°C, recombinant wild-type enzyme
0.029 - 0.059
S-adenosylmethioninamine
0.012 - 0.2
1,4-diaminobutane
0.0022
S-adenosyl-3-methylthio-1-propylamine
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.128 - 0.156
S-adenosylmethioninamine
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.5 - 4.8
S-adenosylmethioninamine
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00005
S-Adenosyl-1,8-diamino-3-thiooctane
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-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
10.3
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W strain
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8.6 - 10.6
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about 65% of maximal activity at pH 8.6 and about 90% of maximal activity at pH 10.6
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37 - 50
sharp drop in activity above optimal temperature 50°C, profile overview
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain MG1655, gene speE
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
spermidine synthase plays a crucial role in cell proliferation and differentiation
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
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
35000
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2 * 35000, sedimentation equilibrium centrifugation and SDS-PAGE
70600
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W strain, sedimentation equilibrium centrifugation
72000
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W strain
73000
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
2 * 36500, 2 * 33823, recombinant His6-tagged enzyme, mass spectrometry, 2 * 33252, His6-tagged enzyme, sequence calculation
dimer
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
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C159A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
D158A
site-directed mutagenesis, inactive mutant
D161A
site-directed mutagenesis, inactive mutant
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 hide
LITERATURE
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
freeze-thawing inactivates
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, partially purified enzyme, several weeks with less than 20% loss of activity
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0-4°C, purified enzyme, 10-20% loss of activity within 6 months
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain SG13009
2000fold purified
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extraction, ammonium sulfate fractionation, chromatography on calcium phosphate cellulose, DEAE-Sephadex, chromatography on hydroxyapatite, disc gel electrophoresis
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using Ni-NTA chromatography
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant overexpression of His6-tagged wild-type and mutant enzymes in Escherichia coli strain SG13009
expressed as a His-tagged fusion protein
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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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
-
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
White Tabor, C.; Tabor, H.
Putrescine aminopropyltransferase (Escherichia coli)
Methods Enzymol.
94
265-270
1983
Escherichia coli
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
Lee, M.J.; Yang, Y.T.; Lin, V.; Huang, H.
Site-directed mutations of the gatekeeping loop region affect the activity of Escherichia coli spermidine synthase
Mol. Biotechnol.
54
572-580
2013
Escherichia coli (P09158), Escherichia coli
Manually annotated by BRENDA team
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