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1gmz

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[[Image:1gmz.png|left|200px]]
 
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{{STRUCTURE_1gmz| PDB=1gmz | SCENE= }}
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==Crystal structure of the D49 phospholipase A2 piratoxin III from Bothrops pirajai.==
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<StructureSection load='1gmz' size='340' side='right'caption='[[1gmz]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1gmz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bothrops_pirajai Bothrops pirajai]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GMZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GMZ FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gmz OCA], [https://pdbe.org/1gmz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gmz RCSB], [https://www.ebi.ac.uk/pdbsum/1gmz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gmz ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PA2H3_BOTPI PA2H3_BOTPI] Snake venom phospholipase A2 (PLA2) that lacks enzymatic activity. Shows high myotoxin activities (PubMed:10395455). Also has anticoagulant activity (PubMed:10395455). 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:10395455</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gm/1gmz_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1gmz ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Snake venoms are rich sources of phospholipase A(2) homologues, both active calcium-binding Asp49 enzymes and essentially inactive Lys49 proteins. They are responsible for multiple pharmacological effects, some of which are dependent on catalytic activity and others of which are not. Here, the 2.4 A X-ray crystal structure of an active Asp49 phospholipase A(2) from the venom of the snake Bothrops pirajai, refined to conventional and free R values of 20.1 and 25.5%, respectively, is reported. Unusually for phospholipases A(2), the dependence of the enzyme rate on the substrate concentration is sigmoidal, implying cooperativity of substrate binding. The unprecedented structural distortion seen for the calcium-binding loop in the present structure may therefore be indicative of a T-state enzyme. An explanation of the interaction between the substrate-binding sites based on the canonical phospholipase A(2) dimer is difficult. However, an alternative putative dimer interface identified in the crystal lattice brings together the calcium-binding loops of neighbouring molecules, along with the C-terminal regions which are disulfide bonded to those loops, thereby offering a possible route of communication between active sites.
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===CRYSTAL STRUCTURE OF THE D49 PHOSPHOLIPASE A2 PIRATOXIN III FROM BOTHROPS PIRAJAI.===
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The structure of the D49 phospholipase A2 piratoxin III from Bothrops pirajai reveals unprecedented structural displacement of the calcium-binding loop: possiblerelationship to cooperative substrate binding.,Rigden DJ, Hwa LW, Marangoni S, Toyama MH, Polikarpov I Acta Crystallogr D Biol Crystallogr. 2003 Feb;59(Pt 2):255-62. Epub 2003, Jan 23. PMID:12554936<ref>PMID:12554936</ref>
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{{ABSTRACT_PUBMED_12554936}}
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==About this Structure==
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<div class="pdbe-citations 1gmz" style="background-color:#fffaf0;"></div>
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[[1gmz]] is a 2 chain structure of [[Phospholipase A2]] with sequence from [http://en.wikipedia.org/wiki/Bothrops_pirajai Bothrops pirajai]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GMZ OCA].
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==See Also==
==See Also==
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*[[Phospholipase A2|Phospholipase A2]]
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*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:012554936</ref><references group="xtra"/>
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__TOC__
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[[Category: Bothrops pirajai]]
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</StructureSection>
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[[Category: Lee, W H.]]
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[[Category: Polikarpov, I.]]
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[[Category: Rigden, D J.]]
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[[Category: Bothrops pirajai]]
[[Category: Bothrops pirajai]]
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[[Category: Hydrolase]]
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[[Category: Large Structures]]
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[[Category: Neurotoxic]]
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[[Category: Lee WH]]
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[[Category: Phospholipase a2]]
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[[Category: Polikarpov I]]
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[[Category: Rigden DJ]]

Current revision

Crystal structure of the D49 phospholipase A2 piratoxin III from Bothrops pirajai.

PDB ID 1gmz

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