1m8r: Difference between revisions

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-[[Image:1m8r.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1m8r", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
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-{{STRUCTURE_1m8r|  PDB=1m8r  |  SCENE=  }}
-'''Crystal Structures of Cadmium-binding Acidic Phospholipase A2 from the Venom of Agkistrodon halys pallas at 1.9 Resolution (crystal grown at pH 7.4)'''
+==Crystal Structures of Cadmium-binding Acidic Phospholipase A2 from the Venom of Agkistrodon halys pallas at 1.9 Resolution (crystal grown at pH 7.4)==
+<StructureSection load='1m8r' size='340' side='right'caption='[[1m8r]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1m8r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gloydius_halys Gloydius halys]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M8R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M8R 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]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BU1:1,4-BUTANEDIOL'>BU1</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</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=1m8r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m8r OCA], [https://pdbe.org/1m8r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m8r RCSB], [https://www.ebi.ac.uk/pdbsum/1m8r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m8r ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PA2A7_GLOHA PA2A7_GLOHA] 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/m8/1m8r_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=1m8r ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Phospholipase A(2) coordinates Ca(2+) ion through three carbonyl oxygen atoms of residues 28, 30, and 32, two carboxyl oxygen atoms of residue Asp49, and two (or one) water molecules, forming seven (or six) coordinate geometry of Ca(2+) ligands. Two crystal structures of cadmium-binding acidic phospholipase A(2) from the venom of Agkistrodon halys Pallas (i.e., Agkistrodon blomhoffii brevicaudus) at different pH values (5.9 and 7.4) were determined to 1.9A resolution by the isomorphous difference Fourier method. The well-refined structures revealed that a Cd(2+) ion occupied the position expected for a Ca(2+) ion, and that the substitution of Cd(2+) for Ca(2+) resulted in detectable changes in the metal-binding region: one of the carboxyl oxygen atoms from residue Asp49 was farther from the metal ion while the other one was closer and there were no water molecules coordinating to the metal ion. Thus the Cd(2+)-binding region appears to have four coordinating oxygen ligands. The cadmium binding to the enzyme induced no other significant conformational change in the enzyme molecule elsewhere. The mechanism for divalent cadmium cation to support substrate binding but not catalysis is discussed.
-==Overview==
+Structures of cadmium-binding acidic phospholipase A2 from the venom of Agkistrodon halys Pallas at 1.9A resolution.,Xu S, Gu L, Jiang T, Zhou Y, Lin Z Biochem Biophys Res Commun. 2003 Jan 10;300(2):271-7. PMID:12504079<ref>PMID:12504079</ref>
-Phospholipase A(2) coordinates Ca(2+) ion through three carbonyl oxygen atoms of residues 28, 30, and 32, two carboxyl oxygen atoms of residue Asp49, and two (or one) water molecules, forming seven (or six) coordinate geometry of Ca(2+) ligands. Two crystal structures of cadmium-binding acidic phospholipase A(2) from the venom of Agkistrodon halys Pallas (i.e., Agkistrodon blomhoffii brevicaudus) at different pH values (5.9 and 7.4) were determined to 1.9A resolution by the isomorphous difference Fourier method. The well-refined structures revealed that a Cd(2+) ion occupied the position expected for a Ca(2+) ion, and that the substitution of Cd(2+) for Ca(2+) resulted in detectable changes in the metal-binding region: one of the carboxyl oxygen atoms from residue Asp49 was farther from the metal ion while the other one was closer and there were no water molecules coordinating to the metal ion. Thus the Cd(2+)-binding region appears to have four coordinating oxygen ligands. The cadmium binding to the enzyme induced no other significant conformational change in the enzyme molecule elsewhere. The mechanism for divalent cadmium cation to support substrate binding but not catalysis is discussed.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-M8R is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Gloydius_halys Gloydius halys]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M8R OCA].
+</div>
+<div class="pdbe-citations 1m8r" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structures of cadmium-binding acidic phospholipase A2 from the venom of Agkistrodon halys Pallas at 1.9A resolution., Xu S, Gu L, Jiang T, Zhou Y, Lin Z, Biochem Biophys Res Commun. 2003 Jan 10;300(2):271-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12504079 12504079]
+*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Gloydius halys]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Gu, L.]]
+[[Category: Gu L]]
-[[Category: Lin, Z.]]
+[[Category: Lin Z]]
-[[Category: Xu, S.]]
+[[Category: Xu S]]
-[[Category: Zhou, Y.]]
+[[Category: Zhou Y]]
-[[Category: Phopholipase a2-metal cation complex]]
-[[Category: Three alpha]]
-[[Category: Two beta]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 00:46:14 2008''