› 3mbb

X-ray diffraction
2.05Å resolution

Crystal structure of StSPL - apo form, after treatment with semicarbazide

Released:
DOI: 10.2210/pdb3mbb/pdb
PDB entry 3mbb coloured by chain, front view.
PDB entry 3mbb coloured by chain, side view.
PDB entry 3mbb coloured by chain, top view.
Source organism: Symbiobacterium thermophilum
Primary publication:
Structure and function of sphingosine-1-phosphate lyase, a key enzyme of sphingolipid metabolism.
Bourquin F, Riezman H, Capitani G, Grütter MG
Structure 18 1054-65 (2010)
PMID: 20696404

Function and Biology Details

Reaction catalysed: 
Sphinganine 1-phosphate = phosphoethanolamine + palmitaldehyde
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-179311 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Putative sphingosine-1-phosphate lyase Chains: A, B
Molecule details ›
Chains: A, B
Length: 514 amino acids
Theoretical weight: 55.65 KDa
Source organism: Symbiobacterium thermophilum
Expression system: Escherichia coli
UniProt:
  • Canonical: Q67PY4 (Residues: 2-507; Coverage: 100%)
Gene name: STH1274
Sequence domains: Pyridoxal-dependent decarboxylase conserved domain
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand PO4 4 x PO4
Ligand EDO 1 x EDO
Ligand NA 1 x NA
1 modified residue:
Ligand TY2 2 x TY2

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 57.65Å b: 126.99Å c: 136.78Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.182 0.181 0.218
Expression system: Escherichia coli

Quick links

Citations

20 review citations

Targeting the sphingosine-1-phosphate axis in cancer, inflammation and beyond.
Kunkel et al. (2013)
19 more

4 mentions without citation

Sphingolipid biosynthesis in man and microbes.
Harrison et al. (2018)
3 more