2py2: Difference between revisions

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-[[Image:2py2.png|left|200px]]
-{{STRUCTURE_2py2|  PDB=2py2  |  SCENE=  }}
+==Structure of Herring Type II Antifreeze Protein==
+<StructureSection load='2py2' size='340' side='right'caption='[[2py2]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2py2]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Clupea_harengus Clupea harengus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PY2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PY2 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]] 1.7&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=2py2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2py2 OCA], [https://pdbe.org/2py2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2py2 RCSB], [https://www.ebi.ac.uk/pdbsum/2py2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2py2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q91992_CLUHA Q91992_CLUHA]
+== 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/py/2py2_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=2py2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In order to survive under extremely cold environments, many organisms produce antifreeze proteins (AFPs). AFPs inhibit the growth of ice crystals and protect organisms from freezing damage. Fish AFPs can be classified into five distinct types based on their structures. Here we report the structure of herring AFP (hAFP), a Ca(2+)-dependent fish type II AFP. It exhibits a fold similar to the C-type (Ca(2+)-dependent) lectins with unique ice-binding features. The 1.7 A crystal structure of hAFP with bound Ca(2+) and site-directed mutagenesis reveal an ice-binding site consisting of Thr96, Thr98 and Ca(2+)-coordinating residues Asp94 and Glu99, which initiate hAFP adsorption onto the [10-10] prism plane of the ice lattice. The hAFP-ice interaction is further strengthened by the bound Ca(2+) through the coordination with a water molecule of the ice lattice. This Ca(2+)-coordinated ice-binding mechanism is distinct from previously proposed mechanisms for other AFPs. However, phylogenetic analysis suggests that all type II AFPs evolved from the common ancestor and developed different ice-binding modes. We clarify the evolutionary relationship of type II AFPs to sugar-binding lectins.
-===Structure of Herring Type II Antifreeze Protein===
+Structure and evolutionary origin of Ca2+-dependent herring type II antifreeze protein.,Liu Y, Li Z, Lin Q, Kosinski J, Seetharaman J, Bujnicki JM, Sivaraman J, Hew CL PLoS ONE. 2007 Jun 20;2(6):e548. PMID:17579720<ref>PMID:17579720</ref>
-{{ABSTRACT_PUBMED_17579720}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2py2" style="background-color:#fffaf0;"></div>
-[[2py2]] is a 6 chain structure of [[Antifreeze protein]] with sequence from [http://en.wikipedia.org/wiki/Clupea_harengus Clupea harengus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PY2 OCA].
 ==See Also==
-*[[Antifreeze protein|Antifreeze protein]]
+*[[Antifreeze protein 3D structures|Antifreeze protein 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:017579720</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Clupea harengus]]
-[[Category: Hew, C L.]]
+[[Category: Large Structures]]
-[[Category: Li, Z.]]
+[[Category: Hew C-L]]
-[[Category: Lin, Q.]]
+[[Category: Li Z]]
-[[Category: Liu, Y.]]
+[[Category: Lin Q]]
-[[Category: Seetharaman, J.]]
+[[Category: Liu Y]]
-[[Category: Sivaraman, J.]]
+[[Category: Seetharaman J]]
-[[Category: Antifreeze protein]]
+[[Category: Sivaraman J]]
-[[Category: Type ii antifreeze protein]]