› 3o4f

X-ray diffraction
2.9Å resolution

Crystal Structure of Spermidine Synthase from E. coli

Released:
DOI: 10.2210/pdb3o4f/pdb
PDB entry 3o4f coloured by chain, front view.
PDB entry 3o4f coloured by chain, side view.
PDB entry 3o4f coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
The crystal structure of Escherichia coli spermidine synthase SpeE reveals a unique substrate-binding pocket.
Zhou X, Chua TK, Tkaczuk KL, Bujnicki JM, Sivaraman J
J Struct Biol 169 277-85 (2010)
PMID: 20051267

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140576 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Polyamine aminopropyltransferase Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 294 amino acids
Theoretical weight: 33.19 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P09158 (Residues: 1-288; Coverage: 100%)
Gene names: JW0117, b0121, speE
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand SO4 31 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P43
Unit cell:
a: 123.11Å b: 123.11Å c: 210.01Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.208 0.241
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Applications of isothermal titration calorimetry in pure and applied research--survey of the literature from 2010.
Ghai et al. (2012)
1 more

1 mention without citation

Spermidine Synthase (SPDS) Undergoes Concerted Structural Rearrangements Upon Ligand Binding - A Case Study of the Two SPDS Isoforms From Arabidopsis thaliana.
Sekula et al. (2019)