› 2ddt

X-ray diffraction
1.8Å resolution

Crystal structure of sphingomyelinase from Bacillus cereus with magnesium ion

Released:
DOI: 10.2210/pdb2ddt/pdb
PDB entry 2ddt coloured by chain, front view.
PDB entry 2ddt coloured by chain, side view.
PDB entry 2ddt coloured by chain, top view.
Source organism: Bacillus cereus
Primary publication:
Structural basis of the sphingomyelin phosphodiesterase activity in neutral sphingomyelinase from Bacillus cereus.
Ago H, Oda M, Takahashi M, Tsuge H, Ochi S, Katunuma N, Miyano M, Sakurai J
J Biol Chem 281 16157-67 (2006)
PMID: 16595670

Function and Biology Details

Reaction catalysed: 
Sphingomyelin + H(2)O = N-acylsphingosine + phosphocholine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145971 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Sphingomyelinase C Chains: A, B
Molecule details ›
Chains: A, B
Length: 306 amino acids
Theoretical weight: 34.34 KDa
Source organism: Bacillus cereus
Expression system: Bacillus subtilis
UniProt:
  • Canonical: P11889 (Residues: 28-333; Coverage: 100%)
Gene name: sph
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase

Ligands and Environments

3 bound ligands:
Ligand MG 4 x MG
Ligand SO4 2 x SO4
Ligand MES 2 x MES
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: P1
Unit cell:
a: 50.844Å b: 50.893Å c: 59.506Å
α: 81.87° β: 81.84° γ: 79.68°
R-values:
R R work R free
0.195 0.193 0.23
Expression system: Bacillus subtilis

Quick links

Citations

10 review citations

Sphingomyelin metabolism at the plasma membrane: implications for bioactive sphingolipids.
Milhas et al. (2010)
9 more

6 mentions without citation

Roles and regulation of neutral sphingomyelinase-2 in cellular and pathological processes.
Shamseddine et al. (2015)
5 more