PDBsum entry 2dds

Hydrolase

PDB id: 2dds

Contents

Protein chains

299 a.a. *

Metals

_CO ×12

Waters ×1116

* Residue conservation analysis

PDB id:

2dds

Name:

Hydrolase

Title:

Crystal structure of sphingomyelinase from bacillus cereus with cobalt ion

Structure:

Sphingomyelin phosphodiesterase. Chain: a, b, c, d. Synonym: sphingomyelinase. Engineered: yes

Source:

Bacillus cereus. Organism_taxid: 1396. Strain: iam 1029. Expressed in: bacillus subtilis. Expression_system_taxid: 1423.

Resolution:

1.80Å R-factor: 0.202 R-free: 0.232

Authors:

H.Ago,M.Oda,M.Takahashi,H.Tsuge,S.Ochi,N.Katunuma,M.Miyano,J.Sakurai, Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

H.Ago et al. (2006). Structural basis of the sphingomyelin phosphodiesterase activity in neutral sphingomyelinase from Bacillus cereus. J Biol Chem, 281, 16157-16167. PubMed id: 16595670 DOI: 10.1074/jbc.M601089200

Date:

02-Feb-06 Release date: 02-May-06

Protein chains

P11889  (PHL2_BACCE) -  Sphingomyelinase C from Bacillus cereus

Seq: 333 a.a.

Struc: 299 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.1.4.12 - sphingomyelin phosphodiesterase.
• Reaction: a sphingomyelin + H2O = phosphocholine + an N-acylsphing-4-enine + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1074/jbc.M601089200

J Biol Chem 281:16157-16167 (2006)

PubMed id: 16595670

Structural basis of the sphingomyelin phosphodiesterase activity in neutral sphingomyelinase from Bacillus cereus.

H.Ago, M.Oda, M.Takahashi, H.Tsuge, S.Ochi, N.Katunuma, M.Miyano, J.Sakurai.

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.

Selected figure(s)

Figure 2.
The edge metal-binding site. The Mg^2+-bound form (A), the Co^2+-bound form (B), and the Ca^2+-bound form (C) bind a divalent metal ion each with octahedral geometry. The |F[o]| – |F[c]| omit electron density map of the Mg^2+-bound form is contoured at 4.5σ. The anomalous difference peaks of the Co^2+- and the Ca^2+-bound forms were contoured at 5σ and 3σ, respectively.

Figure 3.
Effects of divalent metal ions on SM hydrolysis. The values of V[max] and K[m] of hydrolytic activity for the dispersed SM were measured using [N-methyl-^14C]SM. The measured result and the ionic radius of each divalent cation are plotted against the average Lewis acid strength (37). The plots with squares, diamonds, and triangles are the plots of K[m], V[max], and the ionic radius of each divalent cation.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 16157-16167) copyright 2006.

Figures were selected by an automated process.