3rlg

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Loxosceles intermedia phospholipase D isoform 1 H12A mutant

Structural highlights

3rlg is a 1 chain structure with sequence from Loxosceles intermedia. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.6Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A1HA_LOXIN Catalyzes the hydrolysis of sphingomyelin, lysophosphatidylcholine, and lyso-platelet activating factor but not that of phosphatidylcholine. Shows a high enzymatic activity. Induces dermonecrosis, blood vessel permeability and platelet aggregation (PubMed:9790962). Is directly toxic to kidney (PubMed:16005484) and liver (PubMed:18765244). Also induces hemolysis in a complement-dependent manner (PubMed:9790962) as well as in a complement-independent manner. The hemolysis provoked in a complement-independent manner is composed of several steps. The toxin binds to erythrocyte membranes, hydrolyzes membrane phospholipids (sphingomyelin and lysophosphatidylcholine) thus generating metabolism products that cause hemolysis, probably by provoking an increase of calcium inside cells. The calcium influx is due to the opening of L-type calcium channels, since L-type calcium channel blockers inhibit calcium influx (PubMed:21590705).^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Publication Abstract from PubMed

Phospholipases D are the major dermonecrotic component of Loxosceles venom and catalyze the hydrolysis of phospholipids, resulting in the formation of lipid mediators such as ceramide-1-phosphate and lysophosphatidic acid which can induce pathological and biological responses. Phospholipases D can be classified into two classes depending on their catalytic efficiency and the presence of an additional disulfide bridge. In this work, both wild-type and H12A-mutant forms of the class II phospholipase D from L. intermedia venom were crystallized. Wild-type and H12A-mutant crystals were grown under very similar conditions using PEG 200 as a precipitant and belonged to space group P12(1)1, with unit-cell parameters a = 50.1, b = 49.5, c = 56.5 A, beta = 105.9 degrees . Wild-type and H12A-mutant crystals diffracted to maximum resolutions of 1.95 and 1.60 A, respectively.

Crystallization and preliminary X-ray diffraction analysis of a class II phospholipase D from Loxosceles intermedia venom.,Ullah A, de Giuseppe PO, Murakami MT, Trevisan-Silva D, Wille AC, Chaves-Moreira D, Gremski LH, da Silveira RB, Sennf-Ribeiro A, Chaim OM, Veiga SS, Arni RK Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Feb 1;67(Pt, 2):234-6. Epub 2011 Jan 22. PMID:21301094^[7]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Chaim OM, Sade YB, da Silveira RB, Toma L, Kalapothakis E, Chavez-Olortegui C, Mangili OC, Gremski W, von Dietrich CP, Nader HB, Sanches Veiga S. Brown spider dermonecrotic toxin directly induces nephrotoxicity. Toxicol Appl Pharmacol. 2006 Feb 15;211(1):64-77. Epub 2005 Jul 11. PMID:16005484 doi:http://dx.doi.org/S0041-008X(05)00361-3
↑ Kusma J, Chaim OM, Wille AC, Ferrer VP, Sade YB, Donatti L, Gremski W, Mangili OC, Veiga SS. Nephrotoxicity caused by brown spider venom phospholipase-D (dermonecrotic toxin) depends on catalytic activity. Biochimie. 2008 Nov-Dec;90(11-12):1722-36. doi: 10.1016/j.biochi.2008.07.011., Epub 2008 Aug 9. PMID:18760322 doi:http://dx.doi.org/10.1016/j.biochi.2008.07.011
↑ de Oliveira Christoff A, de Oliveira A, Chaim OM, Lugarini D, Bastos Pereira AL, Paludo KS, Queiroz Telles JE, Bracht A, Veiga SS, Acco A. Effects of the venom and the dermonecrotic toxin LiRecDT1 of Loxosceles intermedia in the rat liver. Toxicon. 2008 Nov;52(6):695-704. Epub 2008 Aug 13. PMID:18765244 doi:http://dx.doi.org/S0041-0101(08)00457-1
↑ Chaves-Moreira D, Chaim OM, Sade YB, Paludo KS, Gremski LH, Donatti L, de Moura J, Mangili OC, Gremski W, da Silveira RB, Senff-Ribeiro A, Veiga SS. Identification of a direct hemolytic effect dependent on the catalytic activity induced by phospholipase-D (dermonecrotic toxin) from brown spider venom. J Cell Biochem. 2009 Jul 1;107(4):655-66. doi: 10.1002/jcb.22148. PMID:19455508 doi:http://dx.doi.org/10.1002/jcb.22148
↑ Chaves-Moreira D, Souza FN, Fogaca RT, Mangili OC, Gremski W, Senff-Ribeiro A, Chaim OM, Veiga SS. The relationship between calcium and the metabolism of plasma membrane phospholipids in hemolysis induced by brown spider venom phospholipase-D toxin. J Cell Biochem. 2011 Sep;112(9):2529-40. doi: 10.1002/jcb.23177. PMID:21590705 doi:http://dx.doi.org/10.1002/jcb.23177
↑ Tambourgi DV, Magnoli FC, van den Berg CW, Morgan BP, de Araujo PS, Alves EW, Da Silva WD. Sphingomyelinases in the venom of the spider Loxosceles intermedia are responsible for both dermonecrosis and complement-dependent hemolysis. Biochem Biophys Res Commun. 1998 Oct 9;251(1):366-73. PMID:9790962 doi:http://dx.doi.org/S0006-291X(98)99474-8
↑ Ullah A, de Giuseppe PO, Murakami MT, Trevisan-Silva D, Wille AC, Chaves-Moreira D, Gremski LH, da Silveira RB, Sennf-Ribeiro A, Chaim OM, Veiga SS, Arni RK. Crystallization and preliminary X-ray diffraction analysis of a class II phospholipase D from Loxosceles intermedia venom. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Feb 1;67(Pt, 2):234-6. Epub 2011 Jan 22. PMID:21301094 doi:10.1107/S1744309110050931

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3rlg"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Loxosceles intermedia phospholipase D isoform 1 H12A mutant==
-<StructureSection load='3rlg' size='340' side='right' caption='[[3rlg]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+<StructureSection load='3rlg' size='340' side='right'caption='[[3rlg]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3rlg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Brown_spider Brown spider]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RLG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RLG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3rlg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Loxosceles_intermedia Loxosceles intermedia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RLG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RLG FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3rlh|3rlh]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3rlg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rlg OCA], [https://pdbe.org/3rlg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rlg RCSB], [https://www.ebi.ac.uk/pdbsum/3rlg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rlg ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rlg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rlg OCA], [http://pdbe.org/3rlg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rlg RCSB], [http://www.ebi.ac.uk/pdbsum/3rlg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rlg ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/A1HA_LOXIN A1HA_LOXIN]] Catalyzes the hydrolysis of sphingomyelin, lysophosphatidylcholine, and lyso-platelet activating factor but not that of phosphatidylcholine. Shows a high enzymatic activity. Induces dermonecrosis, blood vessel permeability and platelet aggregation (PubMed:9790962). Is directly toxic to kidney (PubMed:16005484) and liver (PubMed:18765244). Also induces hemolysis in a complement-dependent manner (PubMed:9790962) as well as in a complement-independent manner. The hemolysis provoked in a complement-independent manner is composed of several steps. The toxin binds to erythrocyte membranes, hydrolyzes membrane phospholipids (sphingomyelin and lysophosphatidylcholine) thus generating metabolism products that cause hemolysis, probably by provoking an increase of calcium inside cells. The calcium influx is due to the opening of L-type calcium channels, since L-type calcium channel blockers inhibit calcium influx (PubMed:21590705).<ref>PMID:16005484</ref> <ref>PMID:18760322</ref> <ref>PMID:18765244</ref> <ref>PMID:19455508</ref> <ref>PMID:21590705</ref> <ref>PMID:9790962</ref>
+[https://www.uniprot.org/uniprot/A1HA_LOXIN A1HA_LOXIN] Catalyzes the hydrolysis of sphingomyelin, lysophosphatidylcholine, and lyso-platelet activating factor but not that of phosphatidylcholine. Shows a high enzymatic activity. Induces dermonecrosis, blood vessel permeability and platelet aggregation (PubMed:9790962). Is directly toxic to kidney (PubMed:16005484) and liver (PubMed:18765244). Also induces hemolysis in a complement-dependent manner (PubMed:9790962) as well as in a complement-independent manner. The hemolysis provoked in a complement-independent manner is composed of several steps. The toxin binds to erythrocyte membranes, hydrolyzes membrane phospholipids (sphingomyelin and lysophosphatidylcholine) thus generating metabolism products that cause hemolysis, probably by provoking an increase of calcium inside cells. The calcium influx is due to the opening of L-type calcium channels, since L-type calcium channel blockers inhibit calcium influx (PubMed:21590705).<ref>PMID:16005484</ref> <ref>PMID:18760322</ref> <ref>PMID:18765244</ref> <ref>PMID:19455508</ref> <ref>PMID:21590705</ref> <ref>PMID:9790962</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 21: @@
 ==See Also==
-*[[Phospholipase D|Phospholipase D]]
+*[[Phospholipase D 3D structures|Phospholipase D 3D structures]]
 *[[Sphingomyelinase|Sphingomyelinase]]
 == References ==
@@ Line 28: / Line 27: @@
 __TOC__
 </StructureSection>
-[[Category: Brown spider]]
+[[Category: Large Structures]]
-[[Category: Sphingomyelin phosphodiesterase D]]
+[[Category: Loxosceles intermedia]]
-[[Category: Arni, R K]]
+[[Category: Arni RK]]
-[[Category: Giuseppe, P O]]
+[[Category: Giuseppe PO]]
-[[Category: Murakami, M T]]
+[[Category: Murakami MT]]
-[[Category: Ullah, A]]
+[[Category: Ullah A]]
-[[Category: Veiga, S S]]
+[[Category: Veiga SS]]
-[[Category: Hydrolase]]
-[[Category: Inactive mutant h12a phospholipase d]]
-[[Category: Plc-like phosphodiesterase]]
-[[Category: Tim beta/alpha-barrel]]

3rlg

From Proteopedia

Current revision

Crystal structure of Loxosceles intermedia phospholipase D isoform 1 H12A mutant

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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