2py2: Difference between revisions
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==Structure of Herring Type II Antifreeze Protein== | ==Structure of Herring Type II Antifreeze Protein== | ||
<StructureSection load='2py2' size='340' side='right' caption='[[2py2]], [[Resolution|resolution]] 1.70Å' scene=''> | <StructureSection load='2py2' size='340' side='right'caption='[[2py2]], [[Resolution|resolution]] 1.70Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2py2]] is a 6 chain structure with sequence from [ | <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><td class="sblockLbl"><b>[[ | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7Å</td></tr> | ||
<tr><td class="sblockLbl"><b>[[ | <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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <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> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q91992_CLUHA Q91992_CLUHA] | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/2py2_consurf.spt"</scriptWhenChecked> | <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/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 2py2" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Antifreeze protein|Antifreeze protein]] | *[[Antifreeze protein 3D structures|Antifreeze protein 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
| Line 33: | Line 37: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Clupea harengus]] | [[Category: Clupea harengus]] | ||
[[Category: Hew | [[Category: Large Structures]] | ||
[[Category: Li | [[Category: Hew C-L]] | ||
[[Category: Lin | [[Category: Li Z]] | ||
[[Category: Liu | [[Category: Lin Q]] | ||
[[Category: Seetharaman | [[Category: Liu Y]] | ||
[[Category: Sivaraman | [[Category: Seetharaman J]] | ||
[[Category: Sivaraman J]] | |||
Latest revision as of 04:20, 21 November 2024
Structure of Herring Type II Antifreeze ProteinStructure of Herring Type II Antifreeze Protein
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedIn 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 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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