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Information on EC 2.5.1.16 - spermidine synthase and Organism(s) Homo sapiens and UniProt Accession P19623
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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: Homo sapiens
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
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-
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aminopropyltransferase spermidine synthase
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-
-
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putrescine aminopropyltransferase
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-
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spermidine synthetase
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-
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synthase, spermidine
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-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
S-adenosyl 3-(methylsulfanyl)propylamine + putrescine = S-methyl-5'-thioadenosine + spermidine
S-adenosyl 3-(methylsulfanyl)propylamine + putrescine = S-methyl-5'-thioadenosine + spermidine
Michaelis-Menten kinetics
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S-adenosyl 3-(methylsulfanyl)propylamine + putrescine = S-methyl-5'-thioadenosine + spermidine
general mechanistic hypothesis for the aminopropyl transfer reaction
S-adenosyl 3-(methylsulfanyl)propylamine + putrescine = S-methyl-5'-thioadenosine + spermidine
this mechanism depends on a conserved Asp (residue 173 in hSpdS) in the active site that interacts with the bound amine substrate to deprotonate the attacking nitrogen atom of the amine. This interaction is reinforced by additional interactions of this nitrogen atom with the hydroxyl group of a conserved Tyr (residue 79 in hSpdS) and a backbone carbonyl group (Ser174 in hSpdS). These interactions allow the attack on the methylene carbon atom of the aminopropyl group attached to the sulfonium center of dcAdoMet. Electron transfer to this sulfur atom completes the reaction forming S-methyl-5'-thioadenosine and the polyamine product. The positively charged sulfonium ion is a critical part of the reaction
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
aminopropyl group transfer
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PATHWAY SOURCE
PATHWAYS
BRENDA
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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
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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
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-
-
?
S-adenosylmethioninamine + putrescine
spermidine + 5'-methylthioadenosine
low activity
-
-
?
S-adenosylmethioninamine + putrescine
5'-S-methyl-5'-thioadenosine + spermidine
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-
-
-
?
S-adenosylmethioninamine + putrescine
S-methyl-5'-thioadenosine + spermidine
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-
-
-
?
S-adenosylmethioninamine + putrescine
5'-S-methyl-5'-thioadenosine + spermidine
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-
-
?
S-adenosylmethioninamine + putrescine
5'-S-methyl-5'-thioadenosine + spermidine
the enzyme is highly specific for putrescine
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-
?
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
5'-S-methyl-5'-thioadenosine + spermidine
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-
-
?
S-adenosylmethioninamine + putrescine
S-methyl-5'-thioadenosine + spermidine
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-
-
?
S-adenosylmethioninamine + putrescine
5'-S-methyl-5'-thioadenosine + spermidine
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-
-
-
?
S-adenosylmethioninamine + putrescine
S-methyl-5'-thioadenosine + spermidine
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-
-
-
?
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
decarboxylated S-adenosylhomocysteine
active site binding structure, overview
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
development of a high-throughput assay using homogeneous time-resolved fluorescence based on energy transfer from europium cryptate as a donor to crosslinked allophycocyanin XL665 as an acceptor, involving a competitive immunoassay, overview
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
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spermidine synthhase is responsible for spermdine synthesis from putrescine, the polyamines putrescine, spermidine and spermine are cationic molecules that are found in all eukaryotic cells and are clearly essential to growth and development
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). SPEE_HUMAN
302
0
33825
Swiss-Prot
other Location (Reliability: 2)
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
additional information
additional information
structure analysis, comparison to the enzyme from Thermotoga maritima
additional information
-
structure analysis, comparison to the enzyme from Thermotoga maritima
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant enzyme free or in complex with spermidine, putrescine, 5'-methyl, 5'-deoxymethylthioadenosine, and S-adenosylmethionine, hanging drop vapor diffusion method, 20°C, 10 mg/ml protein solution is mixed with reservoir solution, containing 20-25% PEG 3350, 0.1 M (NH4)2SO4, 0.1 M HEPES-NaOH, pH 7.5, and ligands in a ratio of 1: 5 enzyme-ligand, X-ray diffraction structure determination and analysis at 1.9-2.1 A resolution
spermidine synthase in complex with inhibitor decarboxylated S-adenosylhomocysteine and substrate putrescine, hanging drop vapor diffusion method, mixing of 0.0015 ml of 14 mg/ml protein in 20 mM Tris-HCl, pH 8.0, solution with 0.0015 ml of reservoir solution containing 100 mM Tris-HCl, pH 8.4, 200 mM sodium sulfate, and 20% w/v PEG 3350, 5 mM putrescine and 5 mM decarboxylated S-adenosylhomocysteine, 22°C, X-ray diffraction structure determmination and analysis at 2.0 A resolution
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
generation of transgenic mice overexpressing the human SpdS, the mice are viable and fertile and tissue SpdS activity is increased up to 9fold. This increased SpdS activity does not result in a dramatic elevation of spermidine or spermine levels but leads to a 1.5 to 2fold reduction in tissue spermine:spermidine ratio in heart, muscle and liver tissues with the highest levels of SpdS activity
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80ºC, 20% glycerol, stable for spleen tissue enzyme during storage and freeze-thawings
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme from Escherichia coli strain BL21 (DE3) by nickel affinity chromatography
ammonium sulfate fractionation, chromatography on DEAE-Cellulose, affinity chromatography, 8700fold purified
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of the His-tagged enzyme in Escherichia coli strain BL21 (DE3)
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kajander, E.O.; Kauppinen, L.I.; Pajula, R.L.; Karkola, K.; Eloranta, T.O.
Purification and partial characterization of human polyamine synthases
Biochem. J.
259
879-886
1989
Bos taurus, Homo sapiens, Rattus norvegicus
Enomoto, K.; Nagasaki, T.; Yamauchi, A.; Onoda, J.; Sakai, K.; Yoshida, T.; Maekawa, K.; Kinoshita, Y.; Nishino, I.; Kikuoka, S.; Fukunaga, T.; Kawamoto, K.; Numata, Y.; Takemoto, H.; Nagata, K.
Development of high-throughput spermidine synthase activity assay using homogeneous time-resolved fluorescence
Anal. Biochem.
351
229-240
2006
Homo sapiens
Wu, H.; Min, J.; Ikeguchi, Y.; Zeng, H.; Dong, A.; Loppnau, P.; Pegg, A.E.; Plotnikov, A.N.
Structure and mechanism of spermidine synthases
Biochemistry
46
8331-8339
2007
Homo sapiens (P19623), Homo sapiens, Thermotoga maritima (Q9WZC2), Thermotoga maritima
Shi, C.; Welsh, P.A.; Sass-Kuhn, S.; Wang, X.; McCloskey, D.E.; Pegg, A.E.; Feith, D.J.
Characterization of transgenic mice with overexpression of spermidine synthase
Amino Acids
42
495-505
2012
Homo sapiens
Seckute, J.; McCloskey, D.E.; Thomas, H.J.; Secrist, J.A.; Pegg, A.E.; Ealick, S.E.
Binding and inhibition of human spermidine synthase by decarboxylated S-adenosylhomocysteine
Protein Sci.
20
1836-1844
2011
Plasmodium falciparum, Thermotoga maritima, Homo sapiens (P19623), Homo sapiens
EXTERNAL LINKS (specific for EC-Number 2.5.1.16)
Transporter Classification Database (TCDB): 2.A.1.86.5
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