1y4l
From Proteopedia
(Difference between revisions)
(One intermediate revision not shown.) | |||
Line 3: | Line 3: | ||
<StructureSection load='1y4l' size='340' side='right'caption='[[1y4l]], [[Resolution|resolution]] 1.70Å' scene=''> | <StructureSection load='1y4l' size='340' side='right'caption='[[1y4l]], [[Resolution|resolution]] 1.70Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
- | <table><tr><td colspan='2'>[[1y4l]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/ | + | <table><tr><td colspan='2'>[[1y4l]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bothrops_asper Bothrops asper]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y4L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y4L FirstGlance]. <br> |
- | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=P33:3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL'>P33</scene>, <scene name='pdbligand=SVR:8,8-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFONIC+ACID'>SVR</scene | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7Å</td></tr> |
- | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=P33:3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL'>P33</scene>, <scene name='pdbligand=SVR:8,8-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFONIC+ACID'>SVR</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=1y4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y4l OCA], [https://pdbe.org/1y4l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y4l RCSB], [https://www.ebi.ac.uk/pdbsum/1y4l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y4l ProSAT]</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=1y4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y4l OCA], [https://pdbe.org/1y4l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y4l RCSB], [https://www.ebi.ac.uk/pdbsum/1y4l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y4l ProSAT]</span></td></tr> | ||
</table> | </table> | ||
+ | == Function == | ||
+ | [https://www.uniprot.org/uniprot/PA2H2_BOTAS PA2H2_BOTAS] Snake venom phospholipase A2 homolog that lacks enzymatic activity. Is myotoxic and induces a dose-dependent edema in the mouse foot pad (PubMed:2781572, PubMed:9839670). Also exhibits strong anticoagulant effects by binding to factor Xa (F10) and inhibiting the prothrombinase activity (IC(50) is 3 nM) (PubMed:18062812). In addition, it shows cytotoxic activity to a variety of cell types and bactericidal activity to a variety of Gram-negative and Gram-positive bacteria (PubMed:7886694, PubMed:9654096, PubMed:9920486). Also induces a very rapid release of large amounts of potassium ions and ATP from muscle cells, which accounts for the pain reaction characteristic of viperid envenomations (PubMed:20660736). The released ATP amplifies the effect of the myotoxins, acting as a 'danger signal', which spreads and causes further damage by acting on purinergic receptors (PubMed:20660736). A model of myotoxic mechanism has been proposed: an apo Lys49-PLA2 is activated by the entrance of a hydrophobic molecule (e.g. fatty acid) at the hydrophobic channel of the protein leading to a reorientation of a monomer (By similarity). This reorientation causes a transition between 'inactive' to 'active' states, causing alignment of C-terminal and membrane-docking sites (MDoS) side-by-side and putting the membrane-disruption sites (MDiS) in the same plane, exposed to solvent and in a symmetric position for both monomers (By similarity). The MDoS region stabilizes the toxin on membrane by the interaction of charged residues with phospholipid head groups (By similarity). Subsequently, the MDiS region destabilizes the membrane with penetration of hydrophobic residues (By similarity). This insertion causes a disorganization of the membrane, allowing an uncontrolled influx of ions (i.e. calcium and sodium), and eventually triggering irreversible intracellular alterations and cell death (By similarity).[UniProtKB:I6L8L6]<ref>PMID:18062812</ref> <ref>PMID:1899180</ref> <ref>PMID:20660736</ref> <ref>PMID:2781572</ref> <ref>PMID:7886694</ref> <ref>PMID:9654096</ref> <ref>PMID:9839670</ref> <ref>PMID:9920486</ref> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Line 14: | Line 15: | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y4/1y4l_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y4/1y4l_consurf.spt"</scriptWhenChecked> | ||
- | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </jmolCheckbox> | ||
Line 36: | Line 37: | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
- | [[Category: | + | [[Category: Bothrops asper]] |
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
- | [[Category: Arni | + | [[Category: Arni RK]] |
- | [[Category: Arruda | + | [[Category: Arruda EZ]] |
- | [[Category: Calil-Elias | + | [[Category: Calil-Elias S]] |
- | [[Category: Gutierrez | + | [[Category: Gutierrez JM]] |
- | [[Category: Lomonte | + | [[Category: Lomonte B]] |
- | [[Category: Martinez | + | [[Category: Martinez AB]] |
- | [[Category: Melo | + | [[Category: Melo PA]] |
- | [[Category: Murakami | + | [[Category: Murakami MT]] |
- | [[Category: Tomaz | + | [[Category: Tomaz MA]] |
- | + | ||
- | + | ||
- | + |
Current revision
Crystal structure of Bothrops asper myotoxin II complexed with the anti-trypanosomal drug suramin
|
Categories: Bothrops asper | Large Structures | Arni RK | Arruda EZ | Calil-Elias S | Gutierrez JM | Lomonte B | Martinez AB | Melo PA | Murakami MT | Tomaz MA