1xx1: Difference between revisions

Revision as of 15:36, 3 May 2008

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

OverviewOverview

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 StructureAbout this Structure

1XX1 is a Single protein structure of sequence from Loxosceles laeta. Full crystallographic information is available from OCA.

ReferenceReference

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 Sat May 3 15:36:45 2008

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OCA

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 [[Image:1xx1.gif|left|200px]]
- {{Structure
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+The line below this paragraph, containing "STRUCTURE_1xx1", creates the "Structure Box" on the page.
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+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <span class='plainlinks'>[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] </span>
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-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xx1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xx1 OCA], [http://www.ebi.ac.uk/pdbsum/1xx1 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1xx1 RCSB]</span>
-}}
 '''Structural basis for ion-coordination and the catalytic mechanism of sphingomyelinases D'''
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 [[Category: Murakami, M T.]]
 [[Category: Tambourgi, D V.]]
-[[Category: activity]]
+[[Category: Activity]]
-[[Category: quick cryo-soaking]]
+[[Category: Quick cryo-soaking]]
-[[Category: smase d]]
+[[Category: Smase d]]
-[[Category: structure]]
+[[Category: Structure]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 15:36:45 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:55:45 2008''