2f9r: Difference between revisions

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[[Image:2f9r.gif|left|200px]]<br /><applet load="2f9r" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:2f9r.gif|left|200px]]<br /><applet load="2f9r" size="350" color="white" frame="true" align="right" spinBox="true"

caption="2f9r, resolution 1.85Å" />

'''Crystal structure of the inactive state of the Smase I, a sphingomyelinase D from Loxosceles laeta venom'''<br />

==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.

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 [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Loxosceles_laeta Loxosceles laeta] with MG and EPE as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=2F9R OCA].

2F9R is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Loxosceles_laeta Loxosceles laeta] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=EPE:'>EPE</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F9R OCA].

==Reference==

Line 14:

[[Category: Single protein]]

[[Category: Sphingomyelin phosphodiesterase D]]

[[Category: Arni, R.K.]]

[[Category: Arni, R K.]]

[[Category: Betzel, C.]]

[[Category: Fernandes-Pedrosa, M.F.]]

[[Category: Fernandes-Pedrosa, M F.]]

[[Category: Gabdoulkhakov, A.]]

[[Category: Murakami, M.T.]]

[[Category: Murakami, M T.]]

[[Category: Tambourgi, D.V.]]

[[Category: Tambourgi, D V.]]

[[Category: EPE]]

[[Category: MG]]

Line 27:

[[Category: sphingomyelinase d]]

''Page seeded by [http://~~ispc~~.weizmann.ac.il/oca OCA ] on ~~Wed Nov~~ 21 10:26:~~24 2007~~''

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:19:10 2008''

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@@ Line 1: / Line 1: @@
-[[Image:2f9r.gif|left|200px]]<br /><applet load="2f9r" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:2f9r.gif|left|200px]]<br /><applet load="2f9r" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="2f9r, resolution 1.85&Aring;" />
 '''Crystal structure of the inactive state of the Smase I, a sphingomyelinase D from Loxosceles laeta venom'''<br />
 ==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.
+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==
-F9R is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Loxosceles_laeta Loxosceles laeta] with MG and EPE as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2F9R OCA].
+F9R is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Loxosceles_laeta Loxosceles laeta] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=EPE:'>EPE</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F9R OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Single protein]]
 [[Category: Sphingomyelin phosphodiesterase D]]
-[[Category: Arni, R.K.]]
+[[Category: Arni, R K.]]
 [[Category: Betzel, C.]]
-[[Category: Fernandes-Pedrosa, M.F.]]
+[[Category: Fernandes-Pedrosa, M F.]]
 [[Category: Gabdoulkhakov, A.]]
-[[Category: Murakami, M.T.]]
+[[Category: Murakami, M T.]]
-[[Category: Tambourgi, D.V.]]
+[[Category: Tambourgi, D V.]]
 [[Category: EPE]]
 [[Category: MG]]
@@ Line 27: / Line 27: @@
 [[Category: sphingomyelinase d]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 10:26:24 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:19:10 2008''