1xxw
From Proteopedia
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| - | [[Image:1xxw.gif|left|200px]]<br /><applet load="1xxw" size="350" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="1xxw, resolution 2.70Å" /> | ||
| - | '''Structure of zinc induced heterodimer of two calcium free isoforms of phospholipase A2 from Naja naja sagittifera at 2.7A resolution'''<br /> | ||
| - | == | + | ==Structure of zinc induced heterodimer of two calcium free isoforms of phospholipase A2 from Naja naja sagittifera at 2.7A resolution== |
| + | <StructureSection load='1xxw' size='340' side='right'caption='[[1xxw]], [[Resolution|resolution]] 2.70Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[1xxw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Naja_sagittifera Naja sagittifera]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XXW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XXW 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]] 2.7Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1xxw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xxw OCA], [https://pdbe.org/1xxw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xxw RCSB], [https://www.ebi.ac.uk/pdbsum/1xxw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xxw ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/PA2B1_NAJSG PA2B1_NAJSG] PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. | ||
| + | == 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/xx/1xxw_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=1xxw ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
The crystal structure of a zinc-induced heterodimer of two metal-free isoforms of a cobra venom phospholipase A(2) has been determined at 2.7 angstroms resolution. The crystals belong to space group P4(1), with unit-cell parameters a = b = 65.5, c = 58.4 angstroms, and have a single dimer in the asymmetric unit. The structure has been refined to R(cryst) and R(free) factors of 0.188 and 0.232, respectively. The two isoforms have a sequence identity of 82%. The zinc ion forms a fivefold coordination with a trigonal bipyramidal geometry involving one O atom each from Asp24 and Asn112 from molecule A and Asp24 from molecule B and two water molecules. Both molecules of the dimer are inactive. Molecule A is inactive because Arg31 (B) binds to Asp49 (A), while an acetate ion has displaced the essential water molecule and interacts with His48 (A). On the other hand, Arg31 (A) interacts with the calcium-binding loop of molecule B, resulting in an altered conformation of the loop. The absence of a calcium ion, loss of the essential water molecule and the altered conformation of the calcium-binding loop may be the reasons for the loss of activity of molecule B. | The crystal structure of a zinc-induced heterodimer of two metal-free isoforms of a cobra venom phospholipase A(2) has been determined at 2.7 angstroms resolution. The crystals belong to space group P4(1), with unit-cell parameters a = b = 65.5, c = 58.4 angstroms, and have a single dimer in the asymmetric unit. The structure has been refined to R(cryst) and R(free) factors of 0.188 and 0.232, respectively. The two isoforms have a sequence identity of 82%. The zinc ion forms a fivefold coordination with a trigonal bipyramidal geometry involving one O atom each from Asp24 and Asn112 from molecule A and Asp24 from molecule B and two water molecules. Both molecules of the dimer are inactive. Molecule A is inactive because Arg31 (B) binds to Asp49 (A), while an acetate ion has displaced the essential water molecule and interacts with His48 (A). On the other hand, Arg31 (A) interacts with the calcium-binding loop of molecule B, resulting in an altered conformation of the loop. The absence of a calcium ion, loss of the essential water molecule and the altered conformation of the calcium-binding loop may be the reasons for the loss of activity of molecule B. | ||
| - | + | Structure of the zinc-induced heterodimer of two calcium-free isoforms of phospholipase A2 from Naja naja sagittifera at 2.7 angstroms resolution.,Jabeen T, Sharma S, Singh N, Singh RK, Verma AK, Paramasivam M, Srinivasan A, Singh TP Acta Crystallogr D Biol Crystallogr. 2005 Mar;61(Pt 3):302-8. Epub 2005, Feb 24. PMID:15735340<ref>PMID:15735340</ref> | |
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| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 1xxw" style="background-color:#fffaf0;"></div> | |
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| - | + | ==See Also== | |
| + | *[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Naja sagittifera]] | ||
| + | [[Category: Jabeen T]] | ||
| + | [[Category: Paramasivam M]] | ||
| + | [[Category: Sharma S]] | ||
| + | [[Category: Singh N]] | ||
| + | [[Category: Singh RK]] | ||
| + | [[Category: Singh TP]] | ||
| + | [[Category: Srinivasan A]] | ||
| + | [[Category: Verma AK]] | ||
Current revision
Structure of zinc induced heterodimer of two calcium free isoforms of phospholipase A2 from Naja naja sagittifera at 2.7A resolution
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Categories: Large Structures | Naja sagittifera | Jabeen T | Paramasivam M | Sharma S | Singh N | Singh RK | Singh TP | Srinivasan A | Verma AK
