› 2o07

X-ray diffraction
1.89Å resolution

Human spermidine synthase

Released:
DOI: 10.2210/pdb2o07/pdb
PDB entry 2o07 coloured by chain, front view.
PDB entry 2o07 coloured by chain, side view.
PDB entry 2o07 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure and mechanism of spermidine synthases.
Wu H, Min J, Ikeguchi Y, Zeng H, Dong A, Loppnau P, Pegg AE, Plotnikov AN
Biochemistry 46 8331-9 (2007)
PMID: 17585781

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 domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148670 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Spermidine synthase Chains: A, B
Molecule details ›
Chains: A, B
Length: 304 amino acids
Theoretical weight: 34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P19623 (Residues: 1-302; Coverage: 100%)
Gene names: SPS1, SRM, SRML1
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand SPD 2 x SPD
Ligand MTA 2 x MTA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P21
Unit cell:
a: 58.125Å b: 60.663Å c: 86.705Å
α: 90° β: 108.68° γ: 90°
R-values:
R R work R free
0.179 0.176 0.228
Expression system: Escherichia coli

Quick links

Citations

18 review citations

Mammalian polyamine metabolism and function.
Pegg AE. (2009)
17 more

3 mentions without citation

Crystal structure of human spermine synthase: implications of substrate binding and catalytic mechanism.
Wu et al. (2008)
2 more