› 2pt6

X-ray diffraction
2Å resolution

The structure of Plasmodium falciparum spermidine synthase in complex with decarboxylated S-adenosylmethionine

Released:
DOI: 10.2210/pdb2pt6/pdb
PDB entry 2pt6 coloured by chain, front view.
PDB entry 2pt6 coloured by chain, side view.
PDB entry 2pt6 coloured by chain, top view.
Source organism: Plasmodium falciparum 3D7
Primary publication:
Crystal structure of Plasmodium falciparum spermidine synthase in complex with the substrate decarboxylated S-adenosylmethionine and the potent inhibitors 4MCHA and AdoDATO.
Dufe VT, Qiu W, Müller IB, Hui R, Walter RD, Al-Karadaghi S
J Mol Biol 373 167-77 (2007)
PMID: 17822713

Function and Biology Details

Reaction catalysed: 
S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184780 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
PABS domain-containing protein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 321 amino acids
Theoretical weight: 36.64 KDa
Source organism: Plasmodium falciparum 3D7
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8II73 (Residues: 1-321; Coverage: 100%)
Gene name: PF3D7_1129000
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand S4M 3 x S4M
Ligand 1PG 2 x 1PG
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX II BEAMLINE I911-2
Spacegroup: C2
Unit cell:
a: 196.3Å b: 134.18Å c: 48.32Å
α: 90° β: 94.38° γ: 90°
R-values:
R R work R free
0.182 0.18 0.214
Expression system: Escherichia coli

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Citations

9 review citations

Spermine synthase.
Pegg et al. (2010)
8 more

6 mentions without citation

Polyamines in protozoan pathogens.
Phillips MA. (2018)
5 more