2oqd: Difference between revisions

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-{{Seed}}
-[[Image:2oqd.png|left|200px]]
-<!--
+==Crystal Structure of BthTX-II==
-The line below this paragraph, containing "STRUCTURE_2oqd", creates the "Structure Box" on the page.
+<StructureSection load='2oqd' size='340' side='right'caption='[[2oqd]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2oqd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bothrops_jararacussu Bothrops jararacussu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OQD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OQD FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.19&#8491;</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=2oqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oqd OCA], [https://pdbe.org/2oqd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oqd RCSB], [https://www.ebi.ac.uk/pdbsum/2oqd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oqd ProSAT]</span></td></tr>
-{{STRUCTURE_2oqd|  PDB=2oqd  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PA2B2_BOTJR PA2B2_BOTJR] Snake venom phospholipase A2 (PLA2) that shows a moderate enzymatic activity. It induces indirect hemolytic, anticoagulant, and cytotoxic activities. In vivo, it induces muscle necrosis, accompanied by polymorphonuclear cell infiltration, and edema in the mouse paw. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.<ref>PMID:9619591</ref> <ref>PMID:11018293</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/oq/2oqd_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=2oqd ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A myotoxic Asp49-phospholipase A2 (Asp49-PLA2) with low catalytic activity (BthTX-II from Bothrops jararacussu venom) was crystallized and the molecular-replacement solution has been obtained with a dimer in the asymmetric unit. The quaternary structure of BthTX-II resembles the myotoxic Asp49-PLA2 PrTX-III (piratoxin III from B. pirajai venom) and all non-catalytic and myotoxic dimeric Lys49-PLA2S. Despite of this, BthTX-II is different from the highly catalytic and non-myotoxic BthA-I (acidic PLA2 from B. jararacussu) and other Asp49-PLA2S. BthTX-II structure showed a severe distortion of calcium-binding loop leading to displacement of the C-terminal region. Tyr28 side chain, present in this region, is in an opposite position in relation to the same residue in the catalytic activity Asp49-PLA2S, making a hydrogen bond with the atom O delta 2 of the catalytically active Asp49, which should coordinate the calcium. This high distortion may also be confirmed by the inability of BthTX-II to bind Na+ ions at the Ca2+-binding loop, despite of the crystallization to have occurred in the presence of this ion. In contrast, other Asp49-PLA2S which are able to bind Ca2+ ions are also able to bind Na+ ions at this loop. The comparison with other catalytic, non-catalytic and inhibited PLA2S indicates that the BthTX-II is not able to bind calcium ions; consequently, we suggest that its low catalytic function is based on an alternative way compared with other PLA2S.
-===Crystal Structure of BthTX-II===
+Crystal structure of a myotoxic Asp49-phospholipase A2 with low catalytic activity: Insights into Ca2+-independent catalytic mechanism.,Correa LC, Marchi-Salvador DP, Cintra AC, Sampaio SV, Soares AM, Fontes MR Biochim Biophys Acta. 2008 Apr;1784(4):591-9. Epub 2008 Jan 26. PMID:18261474<ref>PMID:18261474</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2oqd" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18261474}}, adds the Publication Abstract to the page
+*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18261474 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18261474}}
+__TOC__
+</StructureSection>
-==About this Structure==
-OQD is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Bothrops_jararacussu Bothrops jararacussu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OQD OCA].
-==Reference==
-<ref group="xtra">PMID:18261474</ref><references group="xtra"/>
-[[Category: Bothrops jararacussu]]
-[[Category: Cintra, A C.O.]]
-[[Category: Correa, L C.]]
-[[Category: Fontes, M R.M.]]
-[[Category: Marchi-Salvador, D P.]]
-[[Category: Soares, A M.]]
-[[Category: Asp49-phospholipase a2]]
 [[Category: Bothrops jararacussu]]
-[[Category: Bothropstoxin ii]]
+[[Category: Large Structures]]
-[[Category: Bthtx-ii]]
+[[Category: Cintra ACO]]
-[[Category: Hydrolase]]
+[[Category: Correa LC]]
+[[Category: Fontes MRM]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 20:10:57 2009''
+[[Category: Marchi-Salvador DP]]
+[[Category: Soares AM]]