PDBsum entry 2f9r

Hydrolase

PDB id: 2f9r

Contents

Protein chains

285 a.a. *

Ligands

EPE ×3

Metals

_MG ×4

Waters ×510

* Residue conservation analysis

PDB id:

2f9r

Name:

Hydrolase

Title:

Crystal structure of the inactive state of the smase i, a sphingomyelinase d from loxosceles laeta venom

Structure:

Sphingomyelinase d 1. Chain: a, b, c, d. Synonym: sphingomyelinase i, smase i. Engineered: yes

Source:

Loxosceles laeta. Organism_taxid: 58217. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Dimer (from PQS)

Resolution:

1.85Å R-factor: 0.190 R-free: 0.234

Authors:

M.T.Murakami,A.Gabdoulkhakov,M.F.Fernandes-Pedrosa,C.Betzel, D.V.Tambourgi,R.K.Arni

Key ref:

M.T.Murakami et al. (2005). Structural basis for metal ion coordination and the catalytic mechanism of sphingomyelinases D. J Biol Chem, 280, 13658-13664. PubMed id: 15654080 DOI: 10.1074/jbc.M412437200

Date:

06-Dec-05 Release date: 27-Jun-06

Protein chains

Q8I914  (A311_LOXLA) -  Dermonecrotic toxin LlSicTox-alphaIII1i from Loxosceles laeta

Seq: 311 a.a.

Struc: 285 a.a.

Enzyme reactions

• Enzyme class: E.C.4.6.1.- - ?????

DOI no: 10.1074/jbc.M412437200

J Biol Chem 280:13658-13664 (2005)

PubMed id: 15654080

Structural basis for metal ion coordination and the catalytic mechanism of sphingomyelinases D.

M.T.Murakami, M.F.Fernandes-Pedrosa, D.V.Tambourgi, R.K.Arni.

ABSTRACT

Sphingomyelinases D (SMases D) from Loxosceles spider venom are the principal toxins responsible for the manifestation of dermonecrosis, intravascular hemolysis, and acute renal failure, which can result in death. These enzymes catalyze the hydrolysis of sphingomyelin, resulting in the formation of ceramide 1-phosphate and choline or the hydrolysis of lysophosphatidyl choline, generating the lipid mediator lysophosphatidic acid. This report represents the first crystal structure of a member of the sphingomyelinase D family from Loxosceles laeta (SMase I), which has been determined at 1.75-angstrom resolution using the "quick cryo-soaking" technique and phases obtained from a single iodine derivative and data collected from a conventional rotating anode x-ray source. SMase I folds as an (alpha/beta)8 barrel, the interfacial and catalytic sites encompass hydrophobic loops and a negatively charged surface. Substrate binding and/or the transition state are stabilized by a Mg2+ ion, which is coordinated by Glu32, Asp34, Asp91, and solvent molecules. In the proposed acid base catalytic mechanism, His12 and His47 play key roles and are supported by a network of hydrogen bonds between Asp34, Asp52, Trp230, Asp233, and Asn252.

Selected figure(s)

Figure 2.
FIG. 2. A, stereo view of the amino acids and hydrogen bonding in the catalytic and metal ion binding (green sphere) sites; the electron density (blue) in the 2F[o] - F[c] map is contoured at 2.0 . B, schematic representation of the principal hydrogen bonds to the sulfate and metal ion.

Figure 7.
FIG. 7. The proposed mechanism for the catalytic hydrolysis of the sphingomyelin substrate by SMase I, His12, and His47 participate in the reaction as the acid and base. R and R' represent ceramide 1-phosphate and choline, respectively. The figure was generated using ChemSketch (www.acdlabs.com).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 13658-13664) copyright 2005.

Figures were selected by an automated process.