2.5.1.16: spermidine synthase

This is an abbreviated version!
For detailed information about spermidine synthase, go to the full flat file.

Reaction

Synonyms

aminopropyltransferase, aminopropyltransferase spermidine synthase, AtSPDS1, AtSPDS2, MdSPDS1, PAPT, PgSPD, putrescine aminopropyltransferase, Spd synthase, SPDS, SPDS2, SPDSYN, spe-sdh, spe3, SpeE, spermidine synthase, spermidine synthase 1, spermidine synthetase, Spm synthase, SpSyn, Synpcc7942_0628, synthase, spermidine

ECTree

     2 Transferases

         2.5 Transferring alkyl or aryl groups, other than methyl groups

             2.5.1 Transferring alkyl or aryl groups, other than methyl groups (only sub-subclass identified to date)

                2.5.1.16 spermidine synthase

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Results	in table
2	Activating Compound
21026	AA Sequence
5	Application
1	CAS Registry Number
40	Cloned(Commentary)
4	Cofactor
14	Crystallization (Commentary)
93	Disease/ Diagnostics
2	Expression
30	General Information
14	General Stability
10	IC50 Value
198	Inhibitors
6	kcat/KM [mM/s]
10	Ki Value [mM]
51	KM Value [mM]
6	Localization
13	Metals/Ions
53	Molecular Weight [Da]
73	Natural Substrates/ Products (Substrates)
650	Organism
7	Pathway
196	PDB ID
27	pH Optimum
5	pH Range
4	pH Stability
2	pI Value
24	Protein Variants
42	Purification (Commentary)
15	Reaction
1	Reaction Type
125	Reference
118	Source Tissue
18	Specific Activity [micromol/min/mg]
18	Storage Stability
206	Substrates and Products (Substrate)
41	Subunits
80	Synonyms
1	Systematic Name
37	Temperature Optimum [°C]
4	Temperature Range [°C]
8	Temperature Stability [°C]
22	Turnover Number [1/s]

Crystallization

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Crystallization on EC 2.5.1.16 - spermidine synthase

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CRYSTALLIZATION (Commentary)

ORGANISM

UNIPROT

LITERATURE

sitting drop method. Crystallographic date show in detail the structural rearrangements of the enzyme that are required to stabilize ligands within the active site

Arabidopsis thaliana

O48661, Q9ZUB3

759264

-

Caenorhabditis elegans

-

661768

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

Escherichia coli

-

705409

-

Helicobacter pylori

-

660593

purified recombinant His6-tagged enzyme, also as selenomethionine-labeled enzyme, the latter from 0.1 M sodium HEPES, pH 7.5, with 33% PEG 400, two crystals Forms A and B, belonging to the monoclinic space group P21and orthorhombic space group C2221, are grown under different conditions, X-ray diffraction structure determination and analysis at 2.0-2.5 A resolution, multiwavelength anomalous dispersion

Helicobacter pylori

-

677059

sitting drop vapor diffusion at 16°C. Crystal structure of the FliMSpeE complex is determined at 2.7 A resolution

Helicobacter pylori

O25503

759788

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

Homo sapiens

P19623

672272

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

Homo sapiens

P19623

723723

construction of a crystal structure homology model, PDB ID: Q9FS5, for the Plasmodium falciparum enzyme from crystal structure 1JQ3 and 1XJ5, structure-function relationship

Plasmodium falciparum

-

672560

in apo form, in complex with S-adenosylmethioninamine in complex with and two inhibitors, S-adenosyl-1,8-diamino-3-thio-octane and trans-4-methylcyclohexylamine. Binding of S-adenosylmethioninamine stabilizes the conformation of the flexible gatekeeper loop of the enzyme and affects the conformation of the active-site amino acid residues, preparing the protein for binding of the second substrate. Inhibitor S-adenosyl-1,8-diamino-3-thio-octane essentially fills the entire active-site pocket, inhibitor trans-4-methylcyclohexylamine only occupies part of it

Plasmodium falciparum

-

688377

in complex with S-methyl-5'-thioadenosine and putrescine or inhibitors, hanging drop vapor diffusion method, using 0.1 M MES buffer pH 5.6, 0.1 M ammonium sulfate, 27% (w/v) PEG 3350

Plasmodium falciparum

Q8II73

737358

sitting drop vapour diffusion method at 21°C

Synechococcus elongatus

Q31QK9

758761

hanging drop vapour diffusion, multiwavelength anomalous diffraction from selenomethionine containing crystals

Thermotoga maritima

-

639718

in complex with decarboxylated S-adenosylmethionine, trans-4-methylcyclohexylamine and inhibitors, sitting drop vapor diffusion method, using 100 mM bis-Tris pH 5.5-6.5, 200 mM ammonium sulfate, 10-15% (w/v) PEG 4000

Trypanosoma cruzi

Q4DA73

737352