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PDBsum entry 2f9r
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References listed in PDB file
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Key reference
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Title
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Structural basis for metal ion coordination and the catalytic mechanism of sphingomyelinases d.
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Authors
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M.T.Murakami,
M.F.Fernandes-Pedrosa,
D.V.Tambourgi,
R.K.Arni.
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Ref.
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J Biol Chem, 2005,
280,
13658-13664.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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.
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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).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2005,
280,
13658-13664)
copyright 2005.
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