2DDT | pdb_00002ddt

Crystal structure of sphingomyelinase from Bacillus cereus with magnesium ion

• PDB DOI: https://doi.org/10.2210/pdb2DDT/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus cereus
• Expression System: Bacillus subtilis
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2006-02-02 Released: 2006-05-02 
• Deposition Author(s): Ago, H., Oda, M., Tsuge, H., Katunuma, N., Miyano, M., Sakurai, J., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.230 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

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.

(2006) J Biological Chem 281: 16157-16167

• PubMed: 16595670 
• DOI: https://doi.org/10.1074/jbc.M601089200
• Primary Citation Related Structures: 
  2DDR, 2DDS, 2DDT


• PubMed Abstract: 
  

  Sphingomyelinase (SMase) from Bacillus cereus (Bc-SMase) hydrolyzes sphingomyelin to phosphocholine and ceramide in a divalent metal ion-dependent manner. Bc-SMase is a homologue of mammalian neutral SMase (nSMase) and mimics the actions of the endogenous mammalian nSMase in causing differentiation, development, aging, and apoptosis. Thus Bc-SMase may be a good model for the poorly characterized mammalian nSMase. The metal ion activation of sphingomyelinase activity of Bc-SMase was in the order Co2+ > or = Mn2+ > or = Mg2+ >> Ca2+ > or = Sr2+. The first crystal structures of Bc-SMase bound to Co2+, Mg2+, or Ca2+ were determined. The water-bridged double divalent metal ions at the center of the cleft in both the Co2+- and Mg2+-bound forms were concluded to be the catalytic architecture required for sphingomyelinase activity. In contrast, the architecture of Ca2+ binding at the site showed only one binding site. A further single metal-binding site exists at one side edge of the cleft. Based on the highly conserved nature of the residues of the binding sites, the crystal structure of Bc-SMase with bound Mg2+ or Co2+ may provide a common structural framework applicable to phosphohydrolases belonging to the DNase I-like folding superfamily. In addition, the structural features and site-directed mutagenesis suggest that the specific beta-hairpin with the aromatic amino acid residues participates in binding to the membrane-bound sphingomyelin substrate.

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Organizational Affiliation: 
• Structural Biophysics Laboratory, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 69.37 kDa 
• Atom Count: 5,142 
• Modeled Residue Count: 575 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sphingomyelin phosphodiesterase	A, B	306	Bacillus cereus	Mutation(s): 0  EC: 3.1.4.12 Membrane Entity: Yes
UniProt
Find proteins for P11889 (Bacillus cereus) Explore P11889  Go to UniProtKB:  P11889

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	F [auth A], J [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	E [auth A], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	C [auth A], D [auth A], G [auth B], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.230 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.844	α = 81.87
b = 50.893	β = 81.84
c = 59.506	γ = 79.68

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-02 
Deposition Author(s): Ago, H., Oda, M., Tsuge, H., Katunuma, N., Miyano, M., Sakurai, J., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-05-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations