› 2ddr

X-ray diffraction
1.4Å resolution

Crystal structure of sphingomyelinase from Bacillus cereus with calcium ion

Released:
DOI: 10.2210/pdb2ddr/pdb
PDB entry 2ddr coloured by chain, front view.
PDB entry 2ddr coloured by chain, side view.
PDB entry 2ddr 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, C, D
Molecule details ›
Chains: A, B, C, D
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

1 bound ligand:
Ligand CA 8 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL45XU
Spacegroup: P1
Unit cell:
a: 65.43Å b: 72.691Å c: 77.859Å
α: 112.19° β: 89.97° γ: 116.76°
R-values:
R R work R free
0.213 0.213 0.234
Expression system: Bacillus subtilis

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Citations

11 review citations

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

10 mentions without citation

Sphingolipid metabolism and neutral sphingomyelinases.
Airola et al. (2013)
9 more