2f9r
From Proteopedia
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| - | [[Image:2f9r.gif|left|200px]] | + | [[Image:2f9r.gif|left|200px]] |
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| - | '''Crystal structure of the inactive state of the Smase I, a sphingomyelinase D from Loxosceles laeta venom''' | + | {{Structure |
| + | |PDB= 2f9r |SIZE=350|CAPTION= <scene name='initialview01'>2f9r</scene>, resolution 1.85Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID'>EPE</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase_D Sphingomyelin phosphodiesterase D], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.41 3.1.4.41] | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''Crystal structure of the inactive state of the Smase I, a sphingomyelinase D from Loxosceles laeta venom''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2F9R is a [ | + | 2F9R is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Loxosceles_laeta Loxosceles laeta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F9R OCA]. |
==Reference== | ==Reference== | ||
| - | Structural basis for metal ion coordination and the catalytic mechanism of sphingomyelinases D., Murakami MT, Fernandes-Pedrosa MF, Tambourgi DV, Arni RK, J Biol Chem. 2005 Apr 8;280(14):13658-64. Epub 2005 Jan 14. PMID:[http:// | + | Structural basis for metal ion coordination and the catalytic mechanism of sphingomyelinases D., Murakami MT, Fernandes-Pedrosa MF, Tambourgi DV, Arni RK, J Biol Chem. 2005 Apr 8;280(14):13658-64. Epub 2005 Jan 14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15654080 15654080] |
[[Category: Loxosceles laeta]] | [[Category: Loxosceles laeta]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: sphingomyelinase d]] | [[Category: sphingomyelinase d]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:49:49 2008'' |
Revision as of 14:49, 20 March 2008
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| , resolution 1.85Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | and | ||||||
| Activity: | Sphingomyelin phosphodiesterase D, with EC number 3.1.4.41 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of the inactive state of the Smase I, a sphingomyelinase D from Loxosceles laeta venom
Overview
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.
About this Structure
2F9R is a Single protein structure of sequence from Loxosceles laeta. Full crystallographic information is available from OCA.
Reference
Structural basis for metal ion coordination and the catalytic mechanism of sphingomyelinases D., Murakami MT, Fernandes-Pedrosa MF, Tambourgi DV, Arni RK, J Biol Chem. 2005 Apr 8;280(14):13658-64. Epub 2005 Jan 14. PMID:15654080
Page seeded by OCA on Thu Mar 20 16:49:49 2008
