2ph4: Difference between revisions
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< | ==Crystal structure of a novel Arg49 phospholipase A2 homologue from Zhaoermia mangshanensis venom== | ||
<StructureSection load='2ph4' size='340' side='right'caption='[[2ph4]], [[Resolution|resolution]] 2.05Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2ph4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Protobothrops_mangshanensis Protobothrops mangshanensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PH4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PH4 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05Å</td></tr> | |||
-- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=2ph4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ph4 OCA], [https://pdbe.org/2ph4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ph4 RCSB], [https://www.ebi.ac.uk/pdbsum/2ph4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ph4 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/PA2H_PROMB PA2H_PROMB] Snake venom phospholipase A2 homolog that induces myonecrosis, and edema. Has low myotoxic activity.<ref>PMID:16635500</ref> | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ph/2ph4_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ph4 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The venom of Zhaoermia mangshanensis, encountered solely in Mt Mang in China's Hunan Province, exhibits coagulant, phosphodiesterase, l-amino acid oxidase, kallikrein, phospholipase A2 and myotoxic activities. The catalytically inactive PLA2 homolog referred to as zhaoermiatoxin is highly myotoxic and displays high myonecrotic and edema activities. Zhaoermiatoxin possesses a molecular weight of 13,972Da, consists of 121 amino-acid residues cross-linked by seven disulfide bridges and shares high sequence homology with Lys49-PLA2s from the distantly related Asian pitvipers. However, zhaoermiatoxin possesses an arginine residue at position 49 instead of a lysine, thereby suggesting a secondary Lys49-->Arg substitution which results in a catalytically inactive protein. We have determined the first crystal structure of zhaoermiatoxin, an Arg49-PLA2, from Zhaoermia mangshanensis venom at 2.05 angstroms resolution, which represents a novel member of phospholipase A2 family. In this structure, unlike the Lys49 PLA2s, the C-terminus is well ordered and an unexpected non-polarized state of the putative calcium-binding loop due to the flip of Lys122 towards the bulk solvent is observed. The orientation of the Arg-49 side chain results in a similar binding mode to that observed in the Lys49 PLA2s; however, the guadinidium group is tri-coordinated by carbonyl oxygen atoms of the putative calcium-binding loop, whereas the Nzeta atom of lysine is tetra-coordinated as a result of the different conformation adopted by the putative calcium-binding loop. | |||
Crystal structure of a novel myotoxic Arg49 phospholipase A2 homolog (zhaoermiatoxin) from Zhaoermia mangshanensis snake venom: insights into Arg49 coordination and the role of Lys122 in the polarization of the C-terminus.,Murakami MT, Kuch U, Betzel C, Mebs D, Arni RK Toxicon. 2008 Apr;51(5):723-35. Epub 2007 Nov 29. PMID:18295812<ref>PMID:18295812</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2ph4" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]] | |||
*[[Phospholipase A2 homolog|Phospholipase A2 homolog]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
== | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Protobothrops mangshanensis]] | |||
== | [[Category: Arni RK]] | ||
[[Category: Kuch U]] | |||
[[Category: | [[Category: Mebs D]] | ||
[[Category: | [[Category: Murakami MT]] | ||
[[Category: Arni | |||
[[Category: Kuch | |||
[[Category: Mebs | |||
[[Category: Murakami | |||
Latest revision as of 08:25, 17 October 2024
Crystal structure of a novel Arg49 phospholipase A2 homologue from Zhaoermia mangshanensis venomCrystal structure of a novel Arg49 phospholipase A2 homologue from Zhaoermia mangshanensis venom
Structural highlights
FunctionPA2H_PROMB Snake venom phospholipase A2 homolog that induces myonecrosis, and edema. Has low myotoxic activity.[1] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe venom of Zhaoermia mangshanensis, encountered solely in Mt Mang in China's Hunan Province, exhibits coagulant, phosphodiesterase, l-amino acid oxidase, kallikrein, phospholipase A2 and myotoxic activities. The catalytically inactive PLA2 homolog referred to as zhaoermiatoxin is highly myotoxic and displays high myonecrotic and edema activities. Zhaoermiatoxin possesses a molecular weight of 13,972Da, consists of 121 amino-acid residues cross-linked by seven disulfide bridges and shares high sequence homology with Lys49-PLA2s from the distantly related Asian pitvipers. However, zhaoermiatoxin possesses an arginine residue at position 49 instead of a lysine, thereby suggesting a secondary Lys49-->Arg substitution which results in a catalytically inactive protein. We have determined the first crystal structure of zhaoermiatoxin, an Arg49-PLA2, from Zhaoermia mangshanensis venom at 2.05 angstroms resolution, which represents a novel member of phospholipase A2 family. In this structure, unlike the Lys49 PLA2s, the C-terminus is well ordered and an unexpected non-polarized state of the putative calcium-binding loop due to the flip of Lys122 towards the bulk solvent is observed. The orientation of the Arg-49 side chain results in a similar binding mode to that observed in the Lys49 PLA2s; however, the guadinidium group is tri-coordinated by carbonyl oxygen atoms of the putative calcium-binding loop, whereas the Nzeta atom of lysine is tetra-coordinated as a result of the different conformation adopted by the putative calcium-binding loop. Crystal structure of a novel myotoxic Arg49 phospholipase A2 homolog (zhaoermiatoxin) from Zhaoermia mangshanensis snake venom: insights into Arg49 coordination and the role of Lys122 in the polarization of the C-terminus.,Murakami MT, Kuch U, Betzel C, Mebs D, Arni RK Toxicon. 2008 Apr;51(5):723-35. Epub 2007 Nov 29. PMID:18295812[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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