› 6o64

X-ray diffraction
2Å resolution

Crystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 2 (AtSPDS2)

Released:
DOI: 10.2210/pdb6o64/pdb
PDB entry 6o64 coloured by chain, front view.
PDB entry 6o64 coloured by chain, side view.
PDB entry 6o64 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Spermidine Synthase (SPDS) Undergoes Concerted Structural Rearrangements Upon Ligand Binding - A Case Study of the Two SPDS Isoforms From Arabidopsis thaliana.
Sekula B, Dauter Z
OpenAccess logo Front Plant Sci 10 555 (2019)
PMID: 31134111

Function and Biology Details

Reaction catalysed: 
S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129248 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Spermidine synthase 2 Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 305 amino acids
Theoretical weight: 33.46 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O48661 (Residues: 39-340; Coverage: 89%)
Gene names: At1g70310, F17O7.16, SPDSYN2
Sequence domains:

Ligands and Environments

5 bound ligands:
Ligand ACT 5 x ACT
Ligand PEG 10 x PEG
Ligand FMT 3 x FMT
Ligand MLI 4 x MLI
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P21
Unit cell:
a: 75.646Å b: 162.699Å c: 97.494Å
α: 90° β: 100.21° γ: 90°
R-values:
R R work R free
0.177 0.176 0.231
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 citation in other articles

S-adenosylmethionine synthases in plants: Structural characterization of type I and II isoenzymes from Arabidopsis thaliana and Medicago truncatula.
Sekula et al. (2020)
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)