2F9R

Crystal structure of the inactive state of the Smase I, a sphingomyelinase D from Loxosceles laeta venom

Summary for 2F9R

• Entry DOI: 10.2210/pdb2f9r/pdb
• Related: 1XX1
• Descriptor: Sphingomyelinase D 1, MAGNESIUM ION, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ... (4 entities in total)
• Functional Keywords: sphingomyelinase d, catalytic activity, magnesium-binding site, inactive state, hydrolase
• Biological source: Loxosceles laeta
• Cellular location: Secreted: Q8I914
• Total number of polymer chains: 4
• Total formula weight: 129143.95

Authors

Murakami, M.T.,Gabdoulkhakov, A.,Fernandes-Pedrosa, M.F.,Betzel, C.,Tambourgi, D.V.,Arni, R.K. (deposition date: 2005-12-06, release date: 2006-06-27, Last modification date: 2024-10-30)

Primary citation

Murakami, M.T.,Gabdoulkhakov, A.,Fernandes-Pedrosa, M.F.,Tambourgi, D.V.,Arni, R.K.
Structural basis for metal ion coordination and the catalytic mechanism of sphingomyelinases D.
J.Biol.Chem., 280:13658-13664, 2005

PubMed 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.

PubMed: 15654080
DOI: 10.1074/jbc.M412437200

Experimental method

X-RAY DIFFRACTION (1.85 Å)