9ozo: Difference between revisions
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==Structure of phospholipase D BetaIB1i from Sicarius terrosus venom, H47N mutant bound to product and substrate sphingolipids at 2.2 A resolution from a 2-day old crystal== | |||
<StructureSection load='9ozo' size='340' side='right'caption='[[9ozo]], [[Resolution|resolution]] 2.20Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[9ozo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sicarius_terrosus Sicarius terrosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9OZO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9OZO 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]] 2.2Å</td></tr> | |||
[[ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1A43:2-azanylethyl+[(~{E},2~{S},3~{R})-2-(dodecanoylamino)-3-oxidanyl-heptadec-4-enyl]+hydrogen+phosphate'>A1A43</scene>, <scene name='pdbligand=A1A44:N-{(2S,4R,5S)-2-hydroxy-2-oxo-4-[(1E)-tetradec-1-en-1-yl]-1,3,2lambda~5~-dioxaphosphinan-5-yl}dodecanamide'>A1A44</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=9ozo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9ozo OCA], [https://pdbe.org/9ozo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9ozo RCSB], [https://www.ebi.ac.uk/pdbsum/9ozo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9ozo ProSAT]</span></td></tr> | ||
[[ | </table> | ||
[[Category: Binford | == Function == | ||
[[Category: Sundman | [https://www.uniprot.org/uniprot/BIB11_SICTE BIB11_SICTE] Dermonecrotic toxins cleave the phosphodiester linkage between the phosphate and headgroup of certain phospholipids (sphingolipid and lysolipid substrates), forming an alcohol (often choline) and a cyclic phosphate (PubMed:25752604). This toxin acts on lysophosphatidylethanolamine (LPE) and ceramide phosphoethanolamine (CPE) with high activity (PubMed:25752604). This toxin acts on sphingomyelin (SM) with very low activity and is not active on lysophosphatidylserine (LPS), lysophosphatidylcholine (LPC) and lysophosphatidylglycerol (LPG) (PubMed:25752604). It acts by transphosphatidylation, releasing exclusively cyclic phosphate as second products (PubMed:25752604). It is not surprising that spider toxins have affinity for ethanolamine-containing sphingolipids since they are common in insect prey (PubMed:25752604). Induces dermonecrosis, hemolysis, increased vascular permeability, edema, inflammatory response, and platelet aggregation (By similarity).[UniProtKB:P0CE80]<ref>PMID:25752604</ref> | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Sicarius terrosus]] | |||
[[Category: Binford GJ]] | |||
[[Category: Cordes MH]] | |||
[[Category: Montfort WR]] | |||
[[Category: Sundman AK]] | |||
Revision as of 19:28, 4 December 2025
Structure of phospholipase D BetaIB1i from Sicarius terrosus venom, H47N mutant bound to product and substrate sphingolipids at 2.2 A resolution from a 2-day old crystal
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